You don't get someone to love you just because you've paid your dues and "deserve it".

That's exactly it. The whole unstated expectation that the Doctor *owes* Martha anything more than friendship is just really creepy underneath.

I think he is arrogant and flawed, but I don't really see why that's a problem.

I agree that he's arrogant and flawed, but not to the degree that the fandom seems to think he is. His flaws make me love him because they make him a deeper and more interesting character, but so much of fandom reviles him for being imperfect (as if a "perfect" character could ever be interesting).