OK, let's take stock. About the worst thing people have come up with about Falwell is that he said that AIDS was God's punishment on gay people, and that opposing it was wrong. Now, that's pretty insane. He has no basis for knowing this. Even on the assumption that homosexuality is a sin, and that homosexuality is one of a long list of offenses against God that Sodom was guilty of, (that's the most conservative reading that can plausibly be given for the Sodom and Gomorrah passage), the idea that AIDS is punishment for homosexuality is still irrational. It's certainly cringe-worthy. Of course, not all AIDS victims, even back when Falwell said what he did, were gay. What makes it worse is that it seems to be grounds for opposing anti-AIDS efforts. If this ever became public policy, it would cause terrible harm.
But what about Dawkins, or Harris. Dawkins says that bringing a child up as part of a religious community is abusive, comparing it unfavorably with sexual abuse. Yes, he does say that, and he doesn't limit it to people who preach hell-fire to their kids as a means of controlling their conduct. His claims fly in the face of considerable scientific evidence about the effects of religion on children. Since we all agree that the state has an interest in stopping child abuse, and has the right to remove children from abusive parents, this means that he is committed, at least implicitly, to the idea of preventing parents from raising children within their own faith. As I see it, if implemented at the level of public policy, that would bring down the curtain on religious freedom, and on the separation of church and state. In the Soviet Union, they attempted to eliminate religion not by stopping adults from practicing it, but by stopping parents from transmitting it to their children. If this were implemented at the level of public policy it would be disastrous, and sensible atheists should, well, cringe when they hear such a thing.
Which is worse? Does it matter? They're both pretty awful.
My point is that whether you are a theist or an atheist, ideology can get control of your thinking and wipe out your common sense, if you let it. The fact that you are saying it in the name of "reason" or "science" doesn't immunize you from this possibility. If you care about a cause enough, you can die for it, and you can also kill for it. The idea that "religion" is somehow liable to this, while anti-religion is somehow immune, strikes me as preposterous.