As part of the American Mosaic Project, the U of Minnesota did a study on how atheists are perceived in the US:

American’s increasing acceptance of religious diversity doesn’t extend to those who don’t believe in a god, according to a national survey by researchers in the University of Minnesota’s department of sociology.

From a telephone sampling of more than 2,000 households, university researchers found that Americans rate atheists below 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.