Well, let's be honest.
Atheists can and do hate religious folk... Not all, and not all the time, and the hating isn't particular to the atheism. Atheists can hate the way that women or gays or ethnic minorities sometimes hate -- a sort of dull resentment like toothache that one tries to work around, but which occasionally flares into anger at arrant injustice.
It's easy for the godful to attribute the hatred to godlessness, just as it's easy for some men to ascribe women's frustration to mood-swings, but I think it's more often about powerlessness and lack of respect. You can tell because atheistic anger is normally targeted at the same specific behaviours and events.
In fairness, the godful are just as good at hating -- or even better. Monotheism in particular has a track record of extraordinary intolerance. (Which is not to deny that there's huge variation among the godful in this regard.)
I don't know that the problem is religion itself -- though supremacist dogmas don't help -- but I think it is the way that religion -- or rather, an individual's faith -- can get very tribal. Not all religious faith is tribal, but the sort that generates bigotry and unthinking loathing often is.
Tribal faith is an insular, xenophobic, self-serving social construct. The tribal zealot donates his faith, his loyalty and his individuality and in return gains security, belonging and purpose.
A tribesman needs to tribalise his kinfolk and friends, or distance them -- because intimacy requires a high degree of conformity for the tribal sense of security to work. The distancing is essential to maintain the security of tribal boundaries. It generally includes some expression of revulsion or disgust. It might be hostility ('you're an evil and corrupting influence'); it might be condescension ('an infidel can't possibly understand my holy texts'), malicious meddling ('your marriage and customs deserve no legal status'), contempt ('atheists are haters') or neglect ('why should I care what someone not of my tribe needs?'). It might be sublimated into religious ideology ('I don't hate; I just look after my own'), but it will still be noticable to the recipient.
A problem atheists have with the tribally-religious is that tribesmen tend to see everyone in terms of tribe. A tribe must have characteristics they can generalise about, and a foreign tribe is inherently subversive and inferior. ('Atheism is a religion; atheism is an ideology; atheists are secretly communists, libertines or devil-worshippers and they're conspiring to destroy us').
The word 'atheism' was not invented by atheists, but by the tribally religious to mean 'people who live among my tribe but are not of the tribal faith'. Atheists have no need for a term 'living without gods'; neither do people of individual faith. It's the tribally religious who need such terms to work out whether we're in the tribe or outside it. And the main point of that term is to treat atheists collectively -- as a tribe.
The tribally religious sees atheists as a tribe and cannot see them otherwise. And one of the things he'll believe (partly because he expects it, partly because he's told it, partly because he provokes it, and partly because he's inherently xenophobic) is that an atheist must somehow loathe his tribe.
This is eminently unjust: firstly because atheists aren't part of an atheistic tribe, secondly because of the bias involved, thirdly because much of what tribesmen see is their own xenophobia reflected, and finally because much atheistic anger is provoked by bad tribal behaviour in the first place. But a tribesman is an intellectually conservative creature -- his loyalty demands education in the ways of the tribe and not much else. It's almost impossible for a tribesman to see his tribe from the outside-in, or to see a non-tribesman from outside his tribal frame.
What to do about this?
I don't believe that it's terribly helpful to get furious -- though sometimes it's important to let the tribally religious see their impacts. There's no point asking the tribally religious to be an individual and not a tribesman -- he's a tribesman because that's what he wants to be. Neither is insulting the tribe terribly useful either. It just confirms what he expects in the first place -- that anyone outside the tribe is a potential enemy.
The nearest and best answer I have comes from
Steven Pressfield's thoughts on
dealing with Afghani tribesmen -- if you're dealing with someone who's tribally religious and bigoted to boot, you have to pretend to be a tribesman of some (possibly nonexistant) tribe yourself, assert your power and negotiate a deal regarding behaviour -- because tribesmen don't respect individuals,only tribes. And tribes only ever change their thinking from the inside, and only slowly. No-one from outside the tribe can ever negotiate tribal ideology, and an individual without tribe doesn't even rate in a tribesman's eyes.
I believe that this is exactly what tribes of women and ethnic minorities and religious minorities and gay people have done successfully with the thinking of dominant tribes. They had to form tribe before they got any traction at all. But it's harder for atheists because atheism is generally not about tribal belief, but individual thought.
It's not ideal; it's nothing like the way I wish it was. Part of the reason I'm an atheist is that I don't want some ideological tribe telling me what to think. But responding to tribal prejudice with pseudotribal authority is alas the best answer I've unearthed to date for dealing with tribal bigotry.