I can see why people compare the historical situation of homosexuality to the current situation of transsexuality - I've done so myself on occasion. But in one sense they are not at all comparable: homosexuality is not a "condition" that requires any treatment, whereas transsexuality generally needs some kind of medical intervention - pharmaceutical or surgical. This inevitably makes them different in people's minds.
In a lot of ways, it would be more helpful to compare transsexuality to other congenital conditions that used to be untreatable and have stigma attached to them, like thyroid problems. I'd like to think that at some point in the future, people will be able to say "oh yes, I was born with transsexuality, but I had corrective surgery, and now I just need to take hormones to keep me well" and it'll just be seen as a condition like hyperthyroid or something - instead of the "mental condition" it's still regarded as in some quarters.
It's kind of a self-stoking cycle where the stigma attached to being trans causes trans people to present with mental anguish, which is then presumed to be a part of the condition - when in fact it's just a consequence of social conditioning. In cultures where it isn't an issue (or wasn't, pre- Christian intervention), there was no anguish involved, because being trans was just an assimilated part of that culture.
I'm very tired of hearing people make value judgments about how the gay community has higher incidence of unsafe activity and mental health problems, when it's the stigma and homophobia surrounding queer folk that is causing this. Now there is where being transsexual or homosexual has its strongest similarities - in the appalling way we're treated by others.