I agree it's not the most supportive thing a person could say. But it doesn't bother me too much, because: (1) They mean well and are attempting to express non-hostility and admiration, and (2) Yes I am, dammit!
Yes, I get the negative implications. But that's about them: their lack of courage, their implicit acceptance of society's norms, their internalized transphobia. I don't have to accept any of that, because that's their stuff.
It's just one of those clueless, clumsy things that people mumble when they don't know what to say. I am enjoying a great ride here, so I'll cut them some slack and not jump down their throat when they are trying to be accepting.