I don't know. Maybe I react this way because it is too close to home; I have a few old friends who are into all kinds of conspiracy theories and who are pretty much religious nut bags when it comes to that Ancient Astronaut crap. I find it embarrassing, especially since they are grown men with kids and all.
But you're right, as fiction Ancient Astronaut ideas really work well. So many games, movies, comics and novels have built their stories around the idea that we are not from here _or_ that we are the way we are because of extraterrestrial interference.