I think we all use the word cute in slightly different ways. Personally, I would use it to mean pretty, but not the obvious sort of sexy/beautiful look, it's kind of sweet-pretty if you know what I mean. It's not just looks though, you can be cute in your personality too I think.
But, as I said, different guys are likely use the word differently... so it doesn't really have a meaning.
The mystery works both ways. I have been called cute by girls and I'm always bemused by it - do they mean cute like a puppy or what?
when I say cute I mean if you look into my eyes and smile and say 'you're so good at (name something that he's good at here), would you please help me?' then I would melt to the ground. If you were someone sexy or hot who said that then it wouldn't work half as well but I might start to percieve you as cuter. Really, I don't think cute describes how you look but it means you're pretty and you act cute. Hot means you are pretty and act hot, etc.