I want to preface this by saying that I'm jumping into the realm of suppositions, a dangerous path, but one I want to explore. Thus none of the following is any sort of universal truth, merely the impressions I get in observing different reactions to transgendered individuals.
The one thing the religious right has harped on more than anything else is that being gay is a moral abomination, explicitly outlawed by the bible and disgusting in the eyes of their god. They take a platform of righteousness that few have any sort of stomach to debate. Still, there are those that look beyond the archaic words of a millenia old book and follow what they perceive to be the spirit of Christianity in accepting gays.
Things get a little different when it comes to transgendered individuals. There are plenty of liberal, intelligent people that I know who either cannot grasp the complexity of being transgendered or the differences in sex and gender, or just outright disagree with the concept of being transgendered. At times it's almost as if these people have some sort of guilty appeasement in mind after taking a "morally inferior" stance on gays. It's almost as though they say to some imagined conservative party, "well okay we'll disagree on the gays, but we can both agree that being transgendered is wrong."
I understand that it's in human nature to find some sort of common ground, but this kind of appeasement helps no one. It's a setback to the LGBT community because it drives a wedge between some of its members. Worse than having no knowledge is the willingness to misuse some knowledge, and that's what I think we have here.