The medieval Christians followed suit, interpreting other cultures' gods not as humans deified but as demons made divine. Following their cultural beliefs, medieval Christians assumed that every supernatural being not expressly serving Christ was (a) real and (b) Satanic. Today, we have dispensed with the devils and deified men and our fringe theorists instead combine the two classes into extraterrestrial beings, creatures who have the magic powers of demons ("technology") and the supposed flesh-and-blood reality of human beings.
So, it is no surprise that when we look at historical explanations for the evidence claimed for the ancient astronaut theory, we see the same processes at work. Herodotus explained the pyramids as the work of human beings, but by the time we get to Sir Thomas Browne (1605-1682) we see the full flowering of the occult belief in Satanic powers. For him, the pyramids of Egypt were built as the seat of Satan by demons masquerading as Egyptian gods:
Surely if true, these demons were Satan's emissaries, appearing in forms answerable unto Horus and Mompta, the old deities of Egypt, to delude unhappy men. For those dark caves and mummy repositories are Satan's abodes, wherein he speculates and rejoices on human vain-glory, and keeps those kings and conquerors, whom alive he bewitched, whole for that great day, when he will claim his own, and marshall the kings of Nilus and Thebes in sad procession unto the pit. (from Religio Medici, 1643)
Now, how is this really different from the ancient astronaut theorists' claims that the aliens freeze-dried (sorry, "cryogenically preserved") Egyptians to haul away on their spaceships? In both cases, this is a misinterpretation of actual Egyptian religious beliefs through the short-sighted, ethnocentric views of later cultures.
UPDATE 1/31/12: This post contains information that I later learned is not true. Please click here to read the correction.