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.

Atheist: 39.6%
Muslims: 26.3%
Homosexuals: 22.6%
Hispanics: 20%
Conservative Christians: 13.5%
Recent Immigrants: 12.5%
Jews: 7.6%

Atheist: 47.6%
Muslim: 33.5%
African-American 27.2%
Asian-Americans: 18.5%
Hispanics: 18.5%
Jews: 11.8%
Conservative Christians: 6.9%
Whites: 2.3%

Although people may say that they consider atheists inferior because atheists don't believe that civil law should be defined according to some group's conception of what their god wants, I don't think that's the whole story. There are too many religious theists who also want civil law to be secular rather than religious. Instead, I think that a much better case can be made for the idea that atheists are being scapegoated the same way that Catholics and Jews once were: they are treated as social outsiders who create "moral and social disorder."