Well, the thing I note is that there are a lot of studies that say basically the same thing. Atheism is correlated with IQ, it's correlated with level of education, it's correlated with knowledge of religion...I don't know exactly what actual, real world trend that these studies are picking up on, but they're clearly picking up on something, & we're not likely to find out one day that all of those studies were wrong, & there's actually no significant connection between general knowledge & atheism.
Maybe it's not implicit to atheism itself, but theism. A lot of religions actively discourage open-mindedness, because then you might change your mind. If that wasn't the case, then maybe religious people, as a group, would score higher on these things.
And again, group vs. individual. If the article implies that religion is for stupid people, which I don't know because I did not read it, well, that's obviously wrong.