It occurs to me that the problems here are not with specific groups or beliefs but rather with extremes. Those people on the fringes of particular society who beleive in something to the exclusion of all else. It applies to religion, feminism, racism and even BDSM.
Getting off topic with this a little but here is an example. Many years ago, Micheal Moorcock (British fantasy author) was asked to speak at a feminist rally by the organisers. He was booed off the stage because he was a man. This is an author who beleives strongly in women's rights, supports the cause of equality and was one of the first male fantasy authors to put strong and beleivable female characters into his fiction. The question you have to ask there is 'what purpose did those women achieve by potentially alienating a staunch ally from 'the other side'.
I suppose the lesson here is that extremes are where the problems lie and, quite often, these are the most vocal. This means that an awful lot of people see only the extremes. How many people do you think beleive that all Christians are fundametalist anti-evolutionists, that all muslims are terrorists, that all feminists are militant man haters or that all BDSM lifestylers want to lock their daughter in a basement for 20 years? These are clearly ludicrous and yet I have known people who beleive them.
We are influenced by our culture, by the memeplexes that we catch virally as we grow up. Everything we see, learn, read, do builds into a set of values - a memeplex. Religions are very successful memes and they can have a quite strong grip on us. The trick is to analyse everything you think you know and be careful not to fall into dogmatic thought.