We're all alone. grab a hold.
It's an endless play on words if you put it that way. Tolerance is about coexisting with the people you disagree with, but what if the people who disagree with don't want to coexist with you? You'd be tolerant of intolerance, then.
Calling someone intolerant doesn't make you intolerant. I can't bring myself to accept racism, sexism, and homophobia as valid differing viewpoints. Does that make me intolerant? Maybe, but I feel like the true intention of the word would be lost somewhere in that interpretation. Tolerance wouldn't be something to strive for then, because there would be absolutely no point to it. After all, we (as humans) didn't get to where we are scientifically and culturally because we were tolerant (except maybe in the last 50 years).
As for religion, I think it does more harm than good. It teaches people to repeat what they've been told, and not to think for themselves (just my opinion). If we teach creationism in schools, then it should also be okay to teach the idea that aliens and monsters brought about the creation of the earth in schools. There's no scientific evidence for creationism. By definition, it's not a theory, because it can't be tested. Therefore, it's not just a "different viewpoint." It's a personal, scientifically unfounded, objection to a theory with an indescribable mound of evidence in its favor.