I think society tries to put things into contexts they can understand.
Society can understand gay people, now at least. They understand that some men, prefer men, while some women, prefer women. Society continues to have a sad obscession with sexual practice. The truth is, sex is only significant when you're a hormonal teenager. For adults, it's relationships.
Transgender people are, as you point out, in a different situation altogether. But it's difficult for most people to get their head around the notion of a man who wants to cut it off or a woman who want to be a guy. So it puts transgender people into a context it can understand and assumes transgender is extreme gay, or gay that seek to hide it and appear straight.
For my own part I am ready to stand beside any gay person and take whatever they take. It's only ignorance and stupidity, after all.