I'm an atheist, but I have known many very good people who are deeply religious.
There are many good (and bad) people who are christian, muslim, jewish, athiest, and everything else, but that is not a defence of religion any more than the good meat eaters are a defence of meat eating.
I think we need to get past this idea that we can't challenge religion. Attacking religion is not the same as attacking a religious person, just as attacking meat eating is not the same as attacking the person that eats meat. It is a belief the person has. It makes no more sense to say we can't attack religion that it does to say we can't attack meat eating because people will get offended.
We can't get into a situation whereby due to risk of offending people we can't raise these issues. There are people using religion to justify racism, sexism, homophobia and so on every day.
I don't why religions should get a free pass. You are all against homophobia but you most of you will disagree with me or turn the other way if I attack christianity. But in the bible it says: "God created humans to engage in sex only within the arrangement of marriage between a male and a female." and a lot more besides. So you want LGBT equality but you want me to be respectful to Christianity. Good luck with that.
And for the Christians that don't believe things in the bible that disagree with modern science or morality, that is better, but personally I don't see the point.
EDIT: I have changed "respectful to Christians", which is what I originally wrote, to "respectful to Christianity". I think that is a better reflection of what I feel. The original implies that it's unreasonable to ask me to be respectful to Christians, or that I might not be respectful to Christians. I have some issues with the religion, not the people.