Austin Cline (About.com Agnosticism/Atheism) recently asked about the origins of the hatred and bigotry directed at atheists (update: link no longer active) in the U.S. He noted,
The extreme hostility towards atheists in America can probably be traced to two related factors: America's view of itself as a religious nation entrusted with a special mission from God and America's fight against communism in the Cold War.
I think he's right to mention these historical factors, as they are relevant. But I think that there are deeper psychological processes going on here too. Austin mentions scapegoating and refers indirectly to other factors like fear of modernity and loss of privilege. These provide a more comphrensive understanding of what is happening.
For the most part, I'm not convinced that hatred and bigotry against atheists is so different from any other case where an out-group has been demonized and dehumanized. I suspect that the heart of the matter is that atheists have been despised because we are different. We have always been perceived as failing to conform with a standard that has been equated with morality (i.e., religious belief). We aren't just different; we are different in the worst way possible.
To the degree that the hatred and bigotry we face differs from that experienced by other minority groups, this is likely a result of our very existence being viewed as a threat. The only way we can be tolerated is if we remain silent and invisible. As soon as we open our mouths, we pose a danger to an increasingly indefensible belief system.
If we are right, religious believers must be wrong. If a religious believer questioning their faith encounters an atheist, their faith might not survive. Thus, our presence poses a problem for religious believers motivated to maintain their faith and the faith of their children. If only we had that kind of power to disrupt unfounded beliefs!
This post from 2011 was edited to improve clarity in 2022.