What does he mean when he says your cute?

First principle of translating boyspeak for females who haven't clued in on this.

We generally mean what we say, unless we're deliberately lying or being sarcastic. So if a boy says you're cute, the secret hidden meaning in this is most likely that he thinks you're cute.

It may, or may not, mean anything more than this.

The last principle of translating boyspeak: If you want to know what someone means, ask THEM instead of the internet.