I think the main criticism people have with AA is "Why does it have to be bundled with religion?" Why can't it just be about recovery, instead of including God and basically excluding non-Christians? It's that frustration that leads people to extrapolate their hatred from 'AA not being secular is horrible' to 'everything about AA is horrible.'
I think a lot of people are helped by AA. I think a lot of people feel excluded from that help because it is so religious. For goodness sake, it has its own 'big book.' If that's not a kick in the head to atheists, I don't know what is. I don't think people who are used to being surrounded by religion realise just how offensive that is. You get responses like 'it's not just about religion, there's help if you aren't religious' but that doesn't make it any less alienating. Religion has a necessarily 'holier than thou' air about it because they genuinely think you're going to Hell because you aren't of their faith... It's hard to be around people like that, even if they aren't always conscious that this is the doctrine of their organization.
AA is great if you believe in God. Not so much for everyone else.
PS:I know what I've written is probably offensive. I'm not saying AA is a cult. I'm just saying it seems from my outside perspective to be intertwined with religion. A poster above said you have to recite religious scripture... I think if you don't know why that would be uncomfortable for an atheist, you ought to step into our shoes for a day. Of course, I have other reasons for not attending AA, but I really do think if those other reasons were gone the religious aspect would still be upsetting enough to seek other methods.