Most Helpful Girl
Yes, if I say that a guy is cute, I mean that as a compliment.
Most Helpful Guy
Generalising things, men are not supposed to be cute. They're supposed to strong and rugged, and cute is the opposite of that. Going by that sense, no it is not a compliment.
However, if they're complimenting your looks, it probably is a compliment. Moreover, with the world changing and society with it, a guy can be called cute nowadays. So, I guess it depends more upon when they do that.