Why is bashing religion not the equivalent of prejudice against race, sex, sexual orientation, etc.?

I’ve noticed a lot in threads like this, this, this and this, that it seems people who claim to have a rational approach to the issues of the world seem to have not problem with making dismissive and even insulting comments about religion – mostly Christianity.

Why is this not gravely offensive? As a gay man, I see the rational points of a religious argument that although homosexuality may exist homosexual acts are a sin against God, if we work from the assumption that God exists (every rational argument is based on certain assumptions about the nature of reality). However, belief in God is compared to the spaghetti monster by “rationalists” who seem to believe they’re justified in making such gross overgeneralizations without stopping to think about how this is the equivalent of saying, from a societal perspective, “all asians are good at math” or “all gay men sleep around.”

What to people think?