
Persuasion
When it comes to the goal of persuading people to share our beliefs (e.g., helping religious believers realize they don't need their faith, encouraging our fellow atheists to be more willing to engage those who disagree with them), there is some good news. We have a vast scientific literature upon which to draw in order to determine which tactics enhance persuasion and which may harm it.

One observation I suspect every one of you have made in your daily lives is that a speaker's arrogance, self-righteousness, and use of ad hominem attacks against you rarely leads you to change your mind and embrace the speaker's point of view. These behaviors may have other effects (e.g., silencing you, starting a fight), but they rarely lead you to take the speaker's perspective as your own. If we all react this way, chances are good that others will too.
But what about mockery? Wouldn't mocking someone have to be one of the least effective means of persuasion we have? Yes and no. Mocking an individual is probably not going to lead the individual to change his or her mind. However, mocking an individual might have some persuasive impact on others in the audience, at least in some cases.
Of course, persuasion is not always the goal of communication. Perhaps an arrogant, self-righteous atheist who thrives on delivering ad hominem attacks is not interested in persuading anyone. Perhaps this individual has a very different set of goals. Maybe this person is more interested in making a political statement, venting his or her frustration, stirring up controversy for its own sake or to boost the readership of a blog, protecting a fragile ego, or any number of other goals that have little to do with persuasion.
Social Control
While arrogance, self-righteous condemnation of others, and ad hominem attacks may not be particularly effective for persuading an individual, they can be very effective methods of social control. Mockery, mentioned above, can also be quite effective for social control. When an atheist blogger publicly mocks a Christian for leaving a comment dripping with Christianspeak or sending a threatening email, something is being communicated (i.e., these views are not welcome here). Even if the Christian never sees the mockery, the message is not lost on the wider audience.

Unlike effective tactics for persuasion, implementing most methods of social control involves a risk. One who relies on these methods excessively will often be viewed negatively by the community. Obviously, atheists are already viewed quite negatively by the religious majority, but I suspect believers will eventually begin to distinguish between atheists who make some good points and those whose message is nothing but vitriol. At least, I hope so.
As you have seen, excessive reliance on such tactics within the atheist community can do real harm. Part of what we mean by "backlash" in this context is that a critical mass in the community begins to turn on those who have been overusing or abusing such methods. This phenomenon tends to be slow to develop, but once it has developed, it can do lasting damage.
I suspect that some of the squabbles both within the atheist community and in the larger community of atheists and religious believers are due to some confusion between persuasion and social control (e.g., atheists think they are being persuasive but they are instead focusing on social control). Both have their place in how we communicate. Perhaps we will be in a better position to communicate if we clarify our goals and think through how best to achieve them.