I don't have a problem with people believing whatever they want. I'm a "hard" agnostic atheist, and I still go to church, if only to, as my girlfriend puts it, know my enemy.
My problem is with organised religion, because of the assumption that their beiefes can be used to regulate what I do.
The BIG issue is the vocal minority of religions are those who try to force their beliefs on the rest of the world. Like the anti-gay marriage crew who object to it on religious grounds. Or that in the UK the parliament has s set number of seats reserved for bishops. Things like that.
Atheism may occasionally be expressed in an offensive manner, and the most vocal of them tend to be objectionable, often. But The difference is they don't usually say "This is the way things should be," because it's hard to base laws etc on a LACK of scripture.