You are 100% right, make-up doesn't make people smarter! Some people feel a need to wear a mask before they can even go do their laundry ... In their own basement :p I'm an all-natural girl, too. I don't wear make up for anyone! (on special occasions maybe xD) .. I've never been picked on about it though.
If girls start picking on you for not wearing make-up, just say something like "At least I'm comfortable enough with my own face, so I don't need to cover it up with war-paint." or "How do you think a guy feels when he wakes up next to you, and sees your face... On the pillow??" or like you said "Dewd, I'm at school, not a prom.. I don't need to look pretty to do my school work" You TELL 'em!
Cause being natural is beautiful <3