It depends on the context/usage. It's not usually used as 'cute', but it can be used as such.
Angry mother to her child:
Be quite and stop acting silly or you'll be grounded!
Friend to friend, speaking casually:
I thought the play was kind of silly, to be honest...
Shy girl or guy that wants to say cute, but can't:
You're so silly, you know that? d: