Prejudice, pure and simple. America despite its outer secularistic outlook is a religious society nevertheless. According to a poll, 80% of Americans belong and/or profess to belong to a religious denomination. Many Americans are affliliated to religions, if in name only. They view religion as a ticket to familial and social acceptance in addition to an afterlife insurance policy.
Religious dictates have always ruled America from the infamous censorious Hayes Laws in 1934 which curtailed the type of movies that were to played in movie houses until the late 1960s to religious protests against birth control in the earlier part of the 20th century. Religious authorities have always had THEIR say into how things were to be run.
Sadly, atheists are considered to be outsiders and the odd person out in American culture. Atheists are often demonized, ostracized, or worse. Yes, there seems to be a double standard where atheists are concerned. It is FINE to castigate and demonize atheists because they are considered to be personae non gratae. After all, atheists are the MINORITIES and in this society, minorities really don't count for much and considered to be "lesser persons".
Atheists are THE OTHER as far as this religious society goes. Religious people, by inherent strength of their majority, feel that they can do as they please to atheists-that is acceptable. However, to many, the religious majority is sacrosanct in whatever they do.