Every single study that has ever looked at the issue has revealed massive amounts of bigotry and prejudice against atheists in America. The most recent data shows that atheists are more distrusted and despised than any other minority and that an atheist is the least likely person that Americans would vote for in a presidential election. It's not just that atheists are hated, though, but also that atheists seem to represent everything about modernity which Americans dislike or fear.
The most recent study was conducted by the University of Minnesota, which found that atheists ranked lower than "Muslims, recent immigrants, gays and lesbians and other minority groups in 'sharing their vision of American society.' Atheists are also the minority group most Americans are least willing to allow their children to marry." The results from two of the most important questions were:
This group does not at all agree with my vision of American society...
Conservative Christians: 13.5%
Recent Immigrants: 12.5%
I would disapprove if my child wanted to marry a member of this group....
Conservative Christians: 6.9%