From what I've been able to dig up...
President Roosevelt visited Clipperton as part of a tour in 1938 on USS Houston. There doesn't seem to be anything special about the visit, but it does mean the US President and military were aware of the island.
Escorted by the destroyer McDougal, Houston visited Cerros Island (17 July), Magdalena Bay (18 July), San Jose Del Cabo Bay (19 July), Braithwaite Bay (20 July), Clipperton Island (21 July), proceeding thence for the Galapagos Islands, arriving there on the 24th and preparing for the Crossing the Line ceremonies that continued the following morning when the ship crossed the Equator at 0840. After another succession of islands and bays, and fishing trips nearly daily, Houston brought the 5,888 mile cruise to a close at Pensacola, Fla., on 9 August. “This is the third visit I have taken on the HOUSTON in the past four years,” the President told the crew the evening before, “Every moment of the trip has been delightful. I feel the HOUSTON is home.”
USS Atlanta was sent to Clipperton in spring 1942 to check for enemy activity.
After transiting the isthmian waterway, Atlanta then cleared Balboa on 12 April  with orders to reconnoiter Clipperton Island-a tiny, barren, uninhabited atoll about 670 miles southwest of Acapulco, Mexico-in the course of her voyage to the Hawaiian islands, for any signs of enemy activity. Finding none, she ultimately reached Pearl Harbor on 23 April .
The US established a weather station on Clipperton Island with the help of
Patrol Yacht Argus II.
In the second, Argus participated in the establishment of a weather station on Clipperton Island, 670 miles southwest of Acapulco, Mexico. Departing San Francisco on 4 December 1944, with meteorological personnel embarked, the converted yacht reached the island a week later and landed her passengers. With the American colors hoisted over the island, the naval weather station was set up that day, supported at the outset by Argus.
Later, two supply ships, USS Seize and LST-563 grounded on Clipperton. Multiple ships were damaged trying to get them off.
Clipperton Island is located 3000 km due west of the Panama Canal and 1000 km from the nearest land. It's in a good location to monitor activity to and from the Panama Canal. I surmise the US were concerned its position and isolation would make it tempting as a forward base for Japanese seaplanes, submarines, or a radio listening post.
By establishing a weather station the US both prevented its use by the Japanese, and were better able to monitor incoming Pacific storms.
And why 1944? If they wanted to protect it from the Japanese, they were about 3 years late.
I can't say why they waited until 1944 to establish a base, but the Japanese were still a threat to the Canal right up to the end.
Though I'm not sure how aware the US was, Yamamoto proposed in January 1942 building specially designed long-range submarine aircraft carriers to attack the US West Coast and Panama Canal. They actually did this resulting in three I-400 class submarine carrying three attack aircraft each. But by the time they were ready in 1945 the attack was infeasible.
Less ambitiously, the Japanese were fond of using small atolls to resupply submarines and seaplanes. For a relatively small cost, the US could deny the Japanese the only anchorage for 1000 km around.