The problem is the definition of "tolerance". If you go look at the organizations the "We are Family" foundation is affilitated with, and look at their definition of tolerance, you'll find that they don't accept "Not liking gays" or thinking gays will burn in hell as tolerant.
The problem for many people like myself is that we aren't being asked to tolerate, we are being asked to accept, or even openly validate. Expressing our beliefs about homosexuality is to them an act of intolerance.
To me, such flies in the face of REAL tolerance. If we are taught that we should tolerate things because they are okay, then we aren't really learning tolerance. If we are taught to tolerate "non-traditional" families by having our own beliefs shouted down, then we haven't learned to tolerate people we disagree with, we've just been talked into agreeing with them.
When you tell kids that their personal religious beliefs are intolerant when the religion in question is barred from any sort of response, then you are unconstitutionally using public school to combat religious thought. They removed the aspects of the teacher's guide that was a problem for the AFA, and I commend them for it.
Honestly, the only people keeping this from going away are the people that keep bitching about it. For everyone else, including the two sides involved, it was over ages ago...