I came across this section in a recently declassified CIA report on overhead reconnaissance.

High-altitude testing of the U-2 soon led to an unexpected side effect--a tremendous increase in reports of unidentified flying objects (UFOs). In the mid1950s, most commercial airliners flew at altitudes between 10,000 and 20,000 feet and military aircraft like the B-47s operated at altitudes below 40,000 feet. Consequently, once U-2s started flying at altitudes above 60,000 feet, air- traffic controllers began receiving increasing numbers of UFO reports.

Not only did the airline pilots report their sightings to air-traffic controllers, but they and ground-based observers also wrote letters to the Air Force unit at Wright Air Development Command in Dayton charged with investigating such phenomena. This, in turn let to the Air Forces Operation BLUE BOOK. Based at Wright-Patterson, the operation collected all reports of UFO sightings. Air Force investigators then attempted to explain such sightings by linking them to natural phenomena. BLUE BOOK investigators regularly called on the Agencies Project staff in Washington to check reported UFO sightings against U2 flight logs. This enabled investigators to eliminate the majority of UFO reports, although they could not reveal to the letter writers the true cause of the UFO sightings. U-2 and later OXCART flights accounted for more than on half of all UFO reports during the late 1950's and 1960's.

The blue book article on Wikipedia fixates on the minutiae of the program and completely misses the real source of its origins. To re-cap, the Air Force spent decades convincing the American people that the odd aerial phenomena, a surge of new classified aerospace technologies that they had being seeing, were mundane misinterpretations of common occurrences. The most famous of these was the classic "swamp gas" explanation which fostered a deep mistrust among the citizenry and spawned the rise of the the UFO coverup conspiracy theory.

There was a conspiracy by the Air Force to cover up reconnaissance platforms, but certainly not little green men.