I understand where you are coming from when you say, "Atheists are much more likely to be ostracized for their beliefs, but that does not excuse incivility on their part." Even as an atheist, I get annoyed by many of the tactics of hardlined atheists and do wish for more civility in the discussion, but one has to realize that its incredibly hard to be an atheist and even the best of us have days where we can't bite our tongues. Surely as a gay person Andrew has had those moments where he just snapped at someone's homophobia.
Most people are aware that admitting to atheism pretty much bars you from political office, immediately makes your patriotism suspect, can ruin friendships, families, and careers. For reasons of self-preservation, we're often compelled to live "in the closet". In some ways, its tempting to make parallels with other minorities that have been discriminated against over the years, be it based on gender, race, sexual preference, etc. But unlike those groups, we're not forbidden to vote, get married, buy houses, eat at the same restaurants, or any of the other rights other groups had to fight for. In some ways, even I, as an atheist that has been discriminated against time and time again feel like maybe I don't really have any right to complain. But I am treated very differently, and very unfairly, and in a country where "all men are created equal" its time we put an end to that. But what is there to end?
There are no real battles to be fought and won other than general acceptance. Laws about religion are already on the books. There are no acts of Congress that can alleviate the acts of discrimination we face. It is almost purely a battle of intangible social constructs. There are no equivalents to the marches against Prop 8 or riots against faulty elections. There are very few ways to channel the anger, sadness, and frustration of our discrimination.
Every atheist is bound to have a day just bad enough where they explode on some poor believer who pushes too hard and every atheist has felt at time that even the most accepting of believers is tacitly agreeing to the discrimination we face. Sure, I disapprove of many of the less civil tactics some of the more well-known atheists engage in, but I can't say that I don't understand what pushed them to that point. But, in the grander scheme of things, as a group we've yet to do anything as "uncivil" as Stonewall, or the riots we saw during the civil rights movement. Many of these acts are not only forgiven, but celebrated as reasonable responses in the face of discrimination, yet we're screamed at any time an atheist acts like a jerk on TV, writes something a bit testy on a website, or files the occasionally dumb lawsuit.
I dare say that in the history of discriminated groups in this country, atheists have been the most civil and with plenty of room to spare, yet still, we're told that its too much and that we need to calm down and scale it back a notch.
So no, I don't like the incivility some bring to the discussion, but if they didn't, would anyone even be talking about this issues? If everyone remained "civil" it'd get swept up under the rug like it always has in the past. Their incivility might not solve the problem, but it sheds enough of a spotlight on the subject to open a door for the civil conversations that need to happen. Without them I strongly believe the conversation would never happen at all.
As someone who has been guilty of incivility more than once, I agree. Growing up in a society that equates religiosity with morality and patriotism and in a community that equates leaving Orthodoxy with disloyalty, dysfunction, and selfish hedonism and essentially pretends that we no longer exist and don't need to be taken seriously, it's hard not to lash out sometimes.