I really don't see a problem with it. I'm a female player who predominantly plays female characters (although I just had a cool idea for a male character which I think I'm going to make) just because I think of them more easily. When I'm talking to people in game unless I know better I refer to male characters as he and female characters as she. It doesn't mean I think the person behind them is the same gender as their character, it means that I'm at least partially IC most of the time so I'll refer to the character as whatever the owner obviously wants it to be, I don't think it's an issue that deserves a huge amount of thought.
I'm sure that a lot of female avatars are played by men, although CoH isn't as male dominated as some of the more "twitch" based games I play I'd certainly guess there's a lot more men playing than women, but it's not something that I give a lot of thought to in game.
If you make a female character then get offended at being called a woman (or vice versa) then frankly, I'd probably think you were a bit of an idiot.
There's another lady in our SG who normally plays male characters, she has one which is a great hunking tanker wearing just shorts and finds it amusing when the ladies chat her up, but normally it appears to be IC and I'd guess the "ladies" chatting her up are mostly men (get your head round the implication behind that one).
I don't mind if people make slightly forward remarks to some of my characters, one of them I tend to RP as a fairly "forwards" lady, but if I seriously though someone in a game was attempting to chat me the person behin the PC up just because they really thought/knew I was a woman then they'd probably get ignored fairly sharply. This has never happened in CoH, probably because the men I know who play female characters seem to make much more scantily clad costumes than than I do as a general rule.