Every single Democrat I know is religious. Every atheist I know is Libertarian, Republican or independent. Consider: Almost all blacks and a majority Hispanics vote Democrat. Most blacks and Hispanics are religious, Hispanics being overwhelmingly Catholic. CA Prop 8 was passed with black religious support of 70% vs. about 50% for whites, yet those same blacks vote 95% Democrat. The lines aren't as clean as you think.
Religious doesn't mean a vote for conservative or Republican. The main reason more atheists aren't Republican is because the religious wing of the party purposely alienates them. But remember that Republicans have natural allies (and Democrats and RINOs natural enemies) in atheists who tend towards the Randian ideal of government.
There is actually a much better correlation between higher education and voting Republican instead of Democrat.