As to the original question, I guess I'll chime in:
1) IQ is a pretty weak and narrow measure... it is culturally biased, measures knowledge as much or more than it does thinking ability, etc. ...I remember a recent study that suggested that IQs in the last 50 years in the US have gone up something like 10% for African Americans and something like 5% for Caucasians... which only really tells you that our education system might be improving... and that (unsurprisingly, thanks to the civil rights movement) it has improved more for African Americans... it might also say something about childhood nutrition or income disparities or something else... who knows (too many variables). The point is that I think we can safely believe that the raw intelligence of humans has not gone up by 5% to 10% in 50 years... there are other factors showing themselves in these tests... and thus, IQ tests are demonstrably flawed.
2) Association is not by itself demonstrate causation. It is far more likely that both atheism and IQ are associated with some thing(s) which has a hand in causing both directly, or more likely, indirectly... something unidentified.
3) Questions about the relative rationality of atheists vs. theists seems rather silly... remember maxim that: "The more you learn, the less you know." ...meaning the more you learn, the more you realize how little you know. It takes a certain amount of learning to realize how ignorant you are (how ignorant we all are). This can apply to atheists and theists alike. Both have rationality of a kind... and perhaps, given time, naturally lead to an appreciation that the world does not fit neatly into a little box we have set aside for it in our head. On the other hand, I see Young Earth Creationists, for example, as deeply flawed in their rationality (or knowledge or both)... but grouping them with the theists who allow for science and physical laws and such simply isn't fair. Clearly there are very rational people in both the theist and atheist camps. Perhaps it is comparable to the lack of correlation between marital fidelity and effectiveness as a president... Just because one is effective/clear-thinking in one arena may do nothing to help in the other arena. I view theists as having a blind spot of sorts... I imagine they view me quite similarly... but it doesn't reflect on my view of them overall. Everyone has blind spots and weaknesses. I'd like to think that I have a better idea of the nature of the universe than they do... but perhaps I'm just another blind man proclaiming the nature of the elephant (see parable of the six blind men and the elephant). ...that said, I'm not ready to throw my hands up and become a full-on agnostic.
4) When I first saw the heading to this thread, I winced... figuring that it would turn and stay bad... with people saying all kinds of extreme things... People didn't over-react. Dare I say, people here reacted rationally - whether atheist or theist.