It's just my opinion, but to me, someone that would find a person being labeled 'transgender" funny is probably not someone whose opinion I care much about. I know how that sounds, but I'm being honest and that's the truth. As I've gotten older, I've learned to just not let some things and some people piss me off, because they don't deserve my attention.
As far as a hate simulator, well, yeah that's a possibility. But it's been a possibility for a long time. Hateful people will always do what they're going to do - it doesn't make it okay, but if you're prepared for it, at least it's not a surprise, and can be responded to appropriately.
Profiling... Well, if being transgender was a part of their personality, I could see an algorithm (I assume the main character is using his own hacking tools, and would be using one to find information on people) deciding that that was information worth knowing. I would assume that things like this are a part of the game's morality system and are supposed to invoke a reaction. If you get emotionally invested, you're more likely to continue playing.
Finally - WHERE THE HELL IS MY COPY OF WATCHDOGS AMAZON!!? What the fuck?!
Okay, I feel a little better now. If I offended anyone, apologies in advance. I seem to have a knack for it without meaning to. I guess I just have less of a filter than most.