I mostly agree with the OP question.
Look at some of the shows that portray us in a negative light. Jerry Springer, "Hit or Miss", Conan O'Brien and a host of others.
We are shown as freaks, lairs, 'man in a dress', perverts and a host of others. In some areas of the world, we are tolerated, allowed to be, even in some cases we are not noticed. But as individuals, people see us as being "not normal".
In some areas we are vilified, attacked and murdered. We are pointed out, laughed at, things are thrown at us, or nasty words are said. Our true (read chosen) gender is always misspoken. We are called by the opposite pronoun. Our "real" name is printed, even after it has been legally changed.
I am not all sure that it is religion that causes it, although I am sure it is a large part of it. People just didn't true that which is out of their 'Norm'. If they are unsure, uneducated (about transpeople), lead a sheltered life; they will always look at other people with a suspicious eye.
JMHO