The religious people aren't protesting. They're organized, and urging their organization to not give money to someone who's against the organization. This isn't an attack on atheism. Would you go to a movie that you knew was giving money to missionaries? Would you urge fellow atheists to not give missionaries money?
Yeah, or support the Salvation Army, YMCA or YWCA, World Vision (sponsoring children in Africa etc)...
I freely admit I am a "religious" person, a protestant Christian. I believe that the purpose of Christianity is to develop a personal relationship with our Creator. The church, and organized religion, should be a means, and not an end. Too many people see "religion" as a set of codes, memes, structures, rules, and a structure for power and control over other people and societies. Even in the Bible there are countless stories of Jesus himself fighting against "the system" for that very reason.
Or, to put it in another perspective, I choose to use a Mac because it brings me joy and a smile to my face and helps me get my work done. I come read MacRumors to learn more about my Mac and how to use it better and be better informed about Apple and society, and I tell other people they should use a Mac because I genuinely believe they will be better off once they make the switch. I don't do any of this because of any wish to control anyone or gain power and prestige in the forums or hope to become second in command after Steve Jobs, and I don't use a Mac only because I was promised great rewards for doing so or threatened that my life would suffer if I dared to ever so much as look at a Windows PC. I don't tell others about Macs based on a commission I expect to receive on their purchases.
I haven't read the books, or frankly even heard of them until the hype for this movie came out. I intend to see the movie, and I intend to read the books, and I intend to think for myself. I don't think this is too much to ask from anyone, religious or not, Christian or atheist.
When Catholic groups or church groups cry "boycott" it strikes me as being severely counterproductive, both because (a) it stirs up interest in the thing they would rather be quieted, and (b) because it only reinforces the notion that believing in a religion or church requires one to intentionally close himself off to reasoning and logic and opposing viewpoints -- kind of a "la la la I'm not listening!" syndrome. This not only makes us look like irrational nutcases, but the believer who falls for that crap will be in for a rude shock when one day he or she finds that they really can't explain rationally what they believe in or why they believe it.
Or, again, I use a Mac and I can explain to you exactly why, and debate the merits of Macs versus PCs, and indeed can use a PC productively and see the pros and cons of each, as opposed to someone that says "I've always used Apple and I've never even tried a Windows PC and I never will because Macs are just better and they always will be and that's all I ever need to know. And I'm pulling my kids out of school because they use PCs and I only want them to know how to use Macs".
I have a Christian friend who has read the books and could find nothing to protest because, he says, he shares the author's criticisms on certain aspects of organized religion.