The US was very vocal against Japanese aggression in China in the 1930's and early 1940's but said nothing against German aggression in Europe. The US finally placed an embargo on sending oil and iron ore to Japan as a protest but did nothing against Germany. Yet it would seem that China at that time was not a vital interest of the US but Europe, with friendly nations like England and France, was. The embargo finally caused Japan to look for other sources of these vital materials which eventually led to the attack on Pearl Harbor. We declared war on Japan as a result but not on Germany. My question is why did we put up with Germany's actions but not Japan's? I know that we aided England with Lend Lease and such, but we maintained diplomatic relations with Germany and did not protest their actions the way we did with Japan.
There was considerable political opposition to the US becoming involved in European affairs again. Perhaps the most influential of these was Charles Lindbergh and the America First organization he was affiliated with. When you read through his speeches and other non-interventionist, you'll see that their main focus was on Europe. These groups fell silent for the most part after the German declaration of war against the US following Pearl Harbor.
There was less concern about Japan in the general public. For the most part, up until Pearl Harbor, people didn't think an Asian power would pose a threat. They considered the aggressive, yet diplomatic, moves to be sufficient to curb Japanese aggression in Asia. It wasn't seen as a prelude to war as much as things like Lend-Lease and proposed arms sales to Britain were.
As I noted above, Lindbergh's and America First's opinions were the predominate ones when it came to non-interventionism in Europe.
From America First on the Charles Lindbergh site:
The above principles expressed the general thoughts of the movement. The attack on Pearl Harbor shattered the first 2 points, weakened the 3rd and made the last one moot.
Before that attack followed by the German declaration of war, with the memory of WWI and its aftermath still fresh in the minds of middle age and older Americans, many did not want to become entangled in what they saw as another European war. Most were concerned about the rise of Germany as a power in Europe again although there was much division about the way to deal with it. Lindbergh's idea of "impregnable defense" competed with FDR's limited interventionism.
Polling data from the era isn't as accurate as today's polls but they indicated that about 2/3's of the public supported FDR's policies but that America First was gaining support quickly in some regions of the country, enough that the 1942 mid-terms could have caused a switch in opinions in Congress.
Germany was not a DIRECT threat to the United States. There were two reasons. First, Germany had no navy to speak of (unless it captured the British fleet). Second, the U.S. was counting on Britain and France to contain Germany (until May/June 1940).
Japan was a much clearer threat to the United States. First, because there was no counterweight in Asia to Japan. Second, Japan had a real navy, one that actually more powerful than that of the United States BEFORE Pearl Harbor. That disaster was a consequence, not a cause, of U.S. naval inferiority. (Japan overbuilt, and the U.S. underbuilt the 3-5 ratio prescribed by the Washington Naval Treaty.)
If the United States had been able to defend Britain against Germany, it needed only to defeat Japan in order to be "safe." The combined U.S. and British fleets would have deterred an invasion across the Atlantic. On the other hand, an Axis victory scenario would probably have involved a Japanese fleet convoying a victorious German army from Siberia across the Pacific to Alaska and British Columbia.
I don't know where you got the idea that the US was more "vocal against" Japan than the Axis powers. I picked a random week in 1938 (July 15-21) and looked at all the stories on page 1 of the New York Times. There were 8 negative stories on the Axis and 3 negative stories on Japan. And remember this was a time when Japan was actively attacking China, but Germany was not attacking any country.
The US declared war on Japan because they blew up Pearl Harbor and killed over 2400 American citizens, not because we didn't like what they were doing in China.
There are really two issues you raise:
1) The contrast in the American voice (I limit myself to diplomatic and political, since the press was arguably equally anti-Japanese and anti-German) of condemnation of Japanese aggression, versus the lack of same against Germany
2) The apparent contrast in severity of provisions against Japan (in case of the oil embargo) and Germany.
The Illusion of Neutrality: Spring-Summer 1941
Let us begin with the second: as you point out, with the US embargo on export of gasoline and oil in July 1941, there remains only an illusion of neutrality. Japanese nationalists today usually hang their entire narrative of the road to war around this singular act (or the broader story of "ABCD encirclement") to the exclusion of other important elements. It is true that earlier embargoes on aircraft and aviation fuel, scrap steel, and metal ore were interpreted by Japanese diplomats as "unfriendly" acts they are nothing in comparison to the importance of the openly hostile seizure of assets and the economic impact of the termination of all fuel supplies, which at one point made up 80% of Japanese imports. It was a huge blow to the Japanese, and surely played a role in the emperor finally signing off on plans for the attack on Pearl Harbor (begun months before the fuel embargo) finally in November, 1941.
However, US neutrality was even more obviously an illusion in Europe months before the July Japanese embargo, in secret with the commencement of military coordination between the US and the British in early 1941, and in public through the Lend Lease program in March which, in terms of impact, is the closest equivalent to the Japan oil embargo. German U-boats were already targeting US merchant ships since the previous year and in April 1941 the USS Niblack attacks a german U-boat, marking the first hostility between the two military forces in the Atlantic. Consulates in US, Germany, and Italy are mutually closed in June. But why, you ask, not also a full embargo on fuels to Germany as they did with Japan?
I don't have an empirical answer in the form of any contemporary source, but this would simply would not have had more than a symbolic effect. While the US embargo against Japan had immediate and a powerful effect on the Japanese economy, the US was a marginal player in the supply of ore and oil to Germany by 1941. The US dominated supplies of oil to Germany up to 1939 but this was mostly blocked by the UK after 1939 which made Germany depend on Romania and synthetic sources. The German invasion of Norway in 1940 helped secure Swedish ore supplies, while other key metals were coming in through the Balkans. Between 1940-1941, Germany's Soviet ally was a huge supplier of oil under the terms of the German–Soviet Commercial Agreement, and of course, after Germany's invasion of the Soviet Union in June, Soviet oil fields became a major target of the 1942 campaign year.
Problem of Perception and Historiography
At the heart of your question is an understandable perception, reproduced in much of what we read in general histories of:
1) intense American economic and diplomatic pressure on Japan dating back at least as far as 1931, but intensifying gradually, especially after the Panay Incident in December 1937 fortified the political resolve to oppose Japan (helped along with reports on the massacres in Nanjing after its fall earlier that month).
2) An almost exclusive focus in general histories on US policy in Europe as focused on the Congress vs. President debates over US neutrality and isolationism.
So, the easy answer to your question of contrast of treatment is: a neutrality policy pressed by Congress, and an isolation policy which is founded upon an understanding of a particular European historical context - as distinct from a Pacific environment in which US-Japanese naval competition has unfolded without the burden of a WWI precedent to generate powerful cautionary rhetoric. Such an answer would emphasize the need for FDR to temper his personal hatred for the Nazis and secret pressure of friendly nations against the Germans with a public voice that was more in synch with the isolationist rhetoric of congress, and to an ever decreasing level, public opinion. It would focus on his efforts to revise the Neutrality Act or work around it to provide help where he could prior to the spring of 1941.
However, that should not leave you satisfied. The problem is that the historiographical emphasis found in (2) means that we come away with the impression that the US "said nothing" against German aggression, but this is true only if we focus entirely on the word "German"
In other words, the historical debates over the obstacles FDR faced due to isolationism and neutrality provisions clouds the issue somewhat. By the beginning of 1941, at the latest, FDR is increasingly bold in his (verbal) challenge of Germany, with or without the mention of them specifically. You have correctly identified a contrast in the language used in the rhetoric, but it is important to see how these speeches were interpreted and received in the contemporary press, and by European powers who saw merely a veneer of neutrality on top of speeches that were preparing a country for war.
The Three Threats
One last note on the broader context. You have posed the question as one of policy towards Germany vs. Japan, but historians would point out that the policy towards the Soviet Union is a third leg in the tripod that helps us understand the challenges of US foreign policy at the time and one reason why it was harder to unify public opinion, say, in 1939, rather than in 1940-41: public opinion and American strategists saw all three totalitarian states as potential radical threats to the current geopolitical stability (peace). With the alliance between the Germans and the Soviets (1939-1941) made obvious in the wake of the invasion of Poland, not to mention the Soviet invasion of Finland, a sense of moral clarity in Europe was lost for Americans in a way that for the British (tied closely to European powers through alliances) was less critical at this moment. As Akira Iriye puts it:
"The trouble was that by [1938-9] American official and public opinion had become antagonized against all three...Roosevelt wanted to keep his options open so as to prevent collusion between Germany, the Soviet Union, and Japan" (Iriye, 173)
I'm not up to date on the most recent material but relevant secondary sources on this:
Tansill, Charles Callan. Back Door to War: The Roosevelt Foreign Policy, 1933-1941: Roosevelt Foreign Policy, 1933-41. New ed of 1952 ed edition. Westport, Conn: Greenwood Press, 1975.
This early work sparked a debate around the issue you are raising the argument, much contested and debated since, that FDR - blocked from open confrontation with Germany, sought Japan as a "back door" For the purposes of your question, the key chapter is the final one, 26 (XXVI) which makes the argument for the shift in US policy towards Japan.
Divine, Robert A. The Reluctant Belligerent: American Entry Into World War II. New York: John Wiley & Sons, 1965.
Iriye, Akira. The New Cambridge History of American Foreign Relations: Volume 3. Cambridge: Cambridge University Press, 2013.
Good for the general overview, most specifically chapter 11 on the road to Pearl Harbor. Iriye has long been an expert on the US-Japan side of this story (see his "End of Uncertainty" chapter in Power and Culture: The Japanese-American War 1941-1945 for another nice background on the pre-Pearl Harbor overview).
Dallek, Robert. Franklin D. Roosevelt and American Foreign Policy, 1932-1945: With a New Afterword. 2 edition. New York, NY: Oxford University Press, 1995.
Rhodes, Benjamin D. United States Foreign Policy in the Interwar Period, 1918-1941: The Golden Age of American Diplomatic and Military Complacency. Greenwood Publishing Group, 2001.