The Roots of Hatred and Bigotry Against Atheists

Austin Cline (About.com Agnosticism/Atheism) recently asked about the origins of the hatred and bigotry directed at atheistsin the U.S. He notes,
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 certainly relevant. However, I think that there are deeper psychological processes going on. Austin mentions scapegoating and refers indirectly to others like fear of modernity and loss of privilege. These bring us closer to what is likely happening.
For the most part, I’m not so sure that hatred and bigotry against atheists is so different from any other case where an out-group has been demonization 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).
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.
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