Depends on who is using it and how.  If someone who doesn't know me calls me a weeaboo I'm more likely to be upset...kind of like calling someone a nerd.  If my friends says, "You're such a nerd" I'd probably be like "heheh yeah" but if someone I don't know calls me a nerd it seems more malicious because they're judging you without knowing you and likely intending the term to be negative rather than endearing.