I think the key element, as a brilliant author once wrote, is that "Normalcy is a majority concept, the standard of many and not the concept of just one man".
Considering that trans is a far more recent phenomenon - for obvious technical reasons - than homosexuality, and considering the proportion of the global population directly involved is smaller, I'd say gay protagonists will be more easily accepted - or less vehemently bashed. Case in point, we already have main characters having homosexual romances available in RPGs since a few years. Acceptance takes time, and for most people requires familiarity.
Obviously, indie games have more specific demographics and it'll be far easier there, without risking backlash from intended player-base.
Then, for me, it all depends on the setting, for instance if you use a historical context - far trickier to have gay characters in a society that violently represses them, but having characters with obvious homosexual leanings wouldn't be a problem in Ancient Greece (assuming the devs understand the whole context was quite different from 2014 Western countries). Historical setting, apart from the last few decades, makes it practically impossible to have trans characters - unless there's some divine intervention behind it; in a fantasy context, it might work without trouble, and of course if it's a futuristic / sci-fi setting, then anything goes.
But that part was about consistency, historical consistency or consistency within your invented worl, and not acceptance - because that's for me a far more crucial element when judging if a game/story makes sense.