It's an interesting theory that has been around for a good while (although it appears to be picking up again as of late) and I have to admit that even from a sceptical perspective, if we make the assumption that a) There are intelligent forms of life in the universe besides us and b) They are capable of reaching us...
Well, it certainly makes more sense on a scientific level than the beings worshipped in the past being gods. If the so-called "gods" are indeed just other forms of life out there in the cosmos rather than some set of "higher" beings who we can never observe in a scientific manner...well, ahem. Sure, we haven't scientifically proven behind any doubt that "Aliens are out there"(TM) but from a scientific view their existence should be easier to prove than that of the ancient gods.
On a slightly less controversial topic, if various extraterrestrial have had their hands in guiding us in the past, then it might explain the otherwise somewhat unlikely path of development human beings have undergone over the millenia. One has to wonder what purpose these beings had if they were indeed responsible for guidance/development. Common theory is that they may be trying to shape we humans into a less destructive race, especially considering how many 20th and 21st century Encounters contained environment messages for the abductees.