The problem goes both ways, atheists complain about religious folk hurling scripture at them and religious folk complain about atheists hurling Richard Dawkins at them (I suspect a Bible hurts more than The God Delusion if it hits you square in the temple). It's just that religious folk have been doing this for centuries while atheists used to be relatively quiet until the rise of the internet. They're both loud and angry, but the atheists seem new and interesting.
[EDIT: Maybe this is just the view of an Episcopalian who made the mistake of attending an evangelical college, but I suspect a Bible hurts more when thrown because the person doing the throwing was raised by parents who's only hope for fulfillment was to live through their children and as such Junior has powerful quarterback arms. Meanwhile, the atheist became an internet tough guy rather than a real world bully and his throwing arm is about as impressive as the arms of the flying spaghetti monster.]