I think this stemmed partly from the deliberately provocative title of the hugely popular polemic The God Delusion. Perhaps it's research that correlates liberalism and non-belief with IQ. But whatever the root of it, believers seem to think atheists view them as unsophisticated, unintelligent, and uneducated.
Really, I don't get this one. Surely we don't think the problem with the eminent biologist Francis Collins, who helped found the human genome project, is that he's just not the sharpest knife in the drawer. Surely we don't think that devout Christian Kenneth Miller, the evolutionary biologist at Brown who publicly humiliated advocates of Intelligent Design in the infamous Dover trial, that he just needs to go back to college. These guys are obviously highly intelligent, and they're Christians.
But here's the rub: just because someone is intelligent doesn't make them immune from adhering to irrational, even delusional beliefs. intelligent people can be wrong. Like, completely and totally wrong. There's Isaac Newton, who contributed more to modern science than nearly anyone else ever, then spent the rest of his life as an alchemist. There's professional crackpot Frank Tipler, a physicist who wrote the book The Physics of Christianity, in which he claimed that God literally is the cosmic singularity, that God manipulated the carbon in the Shroud of Turin, and that the resurrection of our earthly bodies spoken of in the book of Revelation means that our consciousnesses with be uploaded into the bodies of spacefaring robots (I swear I am not making this up) – and this guy is a professor of physics at Tulane!
Many highly intelligent scientists and philosophers are and have been Christians. Unfortunately, that doesn't make them right. Just as with creationists, conspiracy theorists, global warming deniers, etc, there is often a sort of compartmentalization of ideas, in which certain beliefs are not held to the same standards of skeptical inquiry as most others. The problem with most believers isn't that they're dumb – it's that they're smart enough to know better.