The quiet, nonhostile atheists are not the ones heard about, so this is selection bias. The theists offended probably do meet unjustified hostility from the vocal and hostile atheists, so in this case it's a very weak sign of being deserving.
In some situations, such as leading a group, if you meet unreasonable hostility or dislike everyone, yes, there is something wrong with that your leading abilities. Labeling assholes as such would be making the fundamental attribution error.
Once you met a few hostile Greens, it is easy to take Greenness (disproportionately) as an evidence for hostility. After all, they are Greens, so they must agree with everything those other Greens said; they are just strategically less open about it.
If your group happens to have a Blue majority at given moment, and you find more people like this, you can organize a Blue takeover of the group by declaring a fight against hostility, and by specifying Greenness (and defending Greens) as one of the symptoms of hostility.
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.