GNXP discusses a Richwine piece in The American on relative intelligence of liberals and conservatives. Richwine nicely tips the hat to Charlton's "Clever sillies" hypothesis but suggests rather that IQ will correlate with making a choice one way or the other about the default position we're endowed with, whether ideology, religion, or anything else. Intelligence will then show a correlation with atheism, if only because only folks from the upper tail of the distribution decide to think about it rather than just stick with the default.
This is of course also Satoshi Kanazawa's hypothesis: high IQ will disproportionately select for evolutionarily novel values and preferences. I had great fun spending a couple weeks on evolutionary psychology and political preferences in my graduate public choice class this year. Some fascinating work out there.