This article says, "Religious people are less intelligent than non-believers, according to a new review of 63 scientific studies stretching back over decades." There are various possible explanations offered, such as more education-- or as fundamentalists would put it, secular humanist brainwashing-- less need for the psychological benefits of religion due to higher self-esteem, and the fact that intelligent people are apparently more likely to get married. It's also possible the researchers are dead wrong, which does happen from time to time:-).
But assuming this is true, I think the most likely reason is simply that people who become atheists in this society are likely to be smart, determined, and analytical, simply because they have to swim against the flow of society and shed the mythology that's been inculcated in them since birth. It takes a certain level of smarts to shrug off your cultural conditioning and think for yourself. None of which means that some atheists aren't dumb as plums.