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As the question asks, why did Thomas Jefferson struggle to win the 1800 presidential election against somebody like Aaron Burr?

I would think that, even in his time, Jefferson would have been greatly looked up to by society and would not have such trouble winning the election.

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Because the Republicans knew that New York would be decisive in the 1800 elections, they decided that Burr (a New Yorker) should serve as the Virginian Jefferson’s running mate. According to Gordon Wood, no Republican expected Burr to get the same number of electoral votes as Jefferson (p. 282). In fact, one elector was supposed to abstain from voting for Burr, but somehow the Republican's plans got confused--not surprising, as this was still the early days of national party politics. Burr and Jefferson ended up accidentally getting the same number of votes.

How would this be resolved? Most Federalists wanted to throw the election to Burr. Policy-wise, Burr could have been a Federalist as easily as a Republican. He was much more friendly to banks than Jefferson, for one. To Burr, politics was "fun and honor & profit" (Wood, p. 280). Burr was not averse to patronage, which a Revolutionary like Jefferson would label "corruption." He was no ideologue, but merely someone who saw politics as an activity befitting someone of his pedigree and talent (p. 280).

It was Burr's lack of ideological fervor--his overweening concern for himself--that led Federalists to try to throw the election to Burr. Better Burr (whose own self-interest would lead him to play ball with existing Federalist power structures) than the ideologue Jefferson.

Quoting Wood again (284):

Federalists thought they might be able to convince some congressmen to throw the election to Burr. Indeed, so great was the Federalists' fear of Jefferson that many of them thought that simply electing Burr was the best way of keeping Jefferson out of the presidency. Burr, said the Federalist Theodore Sedgwick of Massachusetts, was a much safer choice than Jefferson. Burr was no no democrat, he was not attached to any foreign nation, and he was not an enthusisast for any sort of theory. He was just an ordinary selfish, interested politician who would promote whatever would benefit him.

Hamilton, although still friendly with Burr as of 1800, did not agree with this assessment. Hamilton remarked that Jefferson "at least had pretensions to character." Burr, on the other hand, "is sanguine enough to hope every thing--daring enough to attempt every thing--wicked enough to scruple nothing." Even though Hamilton knew "if there be a man in the world I ought to hate, it is Jefferson," he thought the country was safer in the hands of a competent and virtuous (if misguided) ideologue like Jefferson than in a reckless self-server like Burr. Accordingly, Hamilton launched a vigorous campaign for Jefferson (p. 284).

But Hamilton's arguments weren't enough, so deeply did most Federalists distrust Jefferson. Congress voted 35 times without resolving the presidential election. Finally, a Delaware Federalist got assurances second-hand that Jefferson reportedly "would preserve the Federalist financial program, maintain the navy, and refrain from dismissing subordinate Federalist officeholders except for cause." This was enough assurance, and on the 36th ballot, some Federalists abstained from voting, which was enough to throw the presidency to Jefferson over Burr (p. 285).

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At the time Burr was one of the best known political leaders in the country and liked across a spectrum of political tastes at the higher levels of society. Jefferson was more of populist with the support of the common farmer. Northeast Federalists who wanted to consolidate power and cut out ordinary people, deeply distrusted Jefferson and preferred Burr. Burr was also an experienced military commander and Jefferson knew nothing of warfare and the US was in the middle of a war with France.

Nowadays, Jefferson is famous and Burr is disgraced, but in 1800 it was Jefferson who had the lesser fame. In fact, the only reason Jefferson got elected was that some shrewd Federalists like Hamilton knew that Burr was actually MORE populist than Jefferson, and they suspected him to be a closet libertarian-like freedom lover (which in fact he later showed himself to be). Therefore, Jefferson was actually the lesser of two evils, so when the Federalists saw they could not win, they supported Jefferson to avoid a possible Manchurian candidate like Burr who probably would have promoted individual liberties and states rights way more than even Jefferson.

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Because the Founding Fathers screwed up. They didn't see the formation of active political parties coming. Every elector voted for 2 men for President, and the second place man became Vice President. All the Democratic-Republicans voted for Jefferson and Burr, so by law the election became a tie and was thrown in the House.

from WIKI

The election exposed one of the flaws in the original Constitution. Members of the Electoral College were authorized by the original Constitution to vote for two names for President. (The two-vote ballot was created in order to try to maximize the possibility that one candidate received votes from a majority of the electors nationwide; the drafters of the Constitution had not anticipated the rise of organized political parties, which made attaining a nationwide majority much easier.) The Democratic-Republicans had planned for one of the electors to abstain from casting his second vote for Aaron Burr, which would have led to Jefferson receiving one electoral vote more than Burr. The plan, however, was mishandled. Each elector who voted for Jefferson also voted for Burr, resulting in a tied electoral vote. The election was then put into the hands of the outgoing House of Representatives, which, after 35 votes in which neither Jefferson nor Burr obtained a majority, elected Jefferson on the 36th ballot.

Realizing the absurdity of the current situation, where running mates have to fight over the Presidency, the rules were amended so that President and Vice President were different tallies by the electors, with one vote for each by the electors. So a party elector can vote for both his party mates and have them take up their jobs smoothly. Only if the overall election ends in a tie between the President or Vice President candidates will that part be thrown into Congress for a tie breaker.

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