Following up on comments to a previous post, I’d say there are two America-specific factors helping drive ordinary Americans’ distrust of atheists. First, in American popular rhetoric, Communism was always associated with atheism (as in "Godless Communist").
Second, a bunch of marginal publicity-seekers, foremost among them Madalyn Murray O’Hair and the American Atheists, came to embody atheism in the U.S. They filed controversial lawsuits, hooked up with fringe political candidates, and were always finagling to appear on television and trade witless insults with equally-belligerent foes.
In America, it’s often not the smartest or most eloquent people who become famous, but rather the people who "give good television." And, alas, that’s what O’Hair did.