Official, institutional bigotry and discrimination against atheists used to be much more prevalent in America. There was a time when the testimony of atheists would not be accepted in courts of law. Several states technically bar atheists from elected office right in their constitutions, though these provisions are no longer enforceable. Atheists today continue to encounter personal bigotry and resulting discrimination, but not so much in the context of social institutions enforcing official policies.
The biggest exception to this shift away from bigotry and towards equal treatment has been the Boy Scouts of America. Although the Boy Scouts' discrimination against gays appears to be most widely known, they discriminate against atheists on basically the same basis. According to the Boy Scouts, atheists cannot be morally straight or the best kinds of citizens; therefore, they have no place in the organization either as scouts or as adult leaders. People who admit to being atheists are kicked out regardless of their past accomplishments -- in other words, the amount of good a person has done either in their lives or in the Boy Scouts is less important than simply not believing in any gods.
It's disturbing that the media has focused on discrimination against gays, ignoring discrimination against atheists. Many of the court cases challenging Boy Scouts' discrimination have been brought by atheists. It was just such a case that went all the way to the Supreme Court and established that the Boy Scouts are technically a private organization which has a right to discriminate against anyone they want and for any reason they want. The fallout from that decision is still developing: as a private organization that discriminates, they have no moral or legal claim to public assistance, support, or endorsement.
This outrages conservatives who want it both ways: they want the Boy Scouts to be private so they can in bigoted discrimination, but they want them to be public in order to obtain lucrative benefits and government support. In effect, they want the Boy Scouts' discrimination to come without social consequences. Their arguments end up trying to make the case that discrimination against gays and atheists is a positive public good which deserves public support.
This image is based on a World War I poster depicting a Boy Scout handing to Lady Liberty a sword inscribed with "Be Prepared" and encouraged people to contribute to the Third Liberty Loan.