Well, look at it this way: The Westboro Baptists, the KKK, the Christian Identity Movement...they're all pretty intolerant. It's their respective claims to fame. And yet somehow, we all tolerate them. We get angry, we wag our collective fingers. But we don't string `em up and put them in jail for their little intolerances.
On the otherhand, my views about the universe differ from my sister the Catholic, my in-laws who are Jewish, and my wife who was Buddhist/Jewish. I didn't have to tolerate them, and they didn't have to tolerate me, because it isn't even a matter of that.
I go to temple once a week. A massive building full of people who don't have to tolerate me, and I don't have to tolerate them. We all look past the insignificant differences and connect with the human being. What I manage to tolerate is the desire to define a person by their beliefs in God, or gods, or reality, or existence, or whatever.
That's why the whole concept of tolerance of atheists being defined as not murdering them so funny. It misses the point entirely. If I'mtolerating people because they don't agree with my religion, or they don't agree with mine, then I think I've missed the point of fellowship completely.