Refusing to go along with the majority is often viewed as a hostile act. Theists and atheists are hardly unique here.
Disagreeing with the majority is often viewed as an arrogant act. Who are you to think you know better than us? Again, theists and atheists are hardly unique here.
http://blip.tv/tech-love-live/osb09-donnie-berkholz-assholes-are-killing-your-project-2464449
This is specifically about why it's important to get assholes out of open source projects, but it applies in general. It includes an analysis of the social cost of keeping people around who frequently make other people unhappy, and in particular a way to balance the social costs (distraction, people doing much less work or leaving, useful volunteers not joining, assholes recruiting other assholes, etc.) of assholes against the useful work some of them do.