Ha, I have a friend who used to say that to me regularly, and I always spin it by saying "oh, so I don't look nice/pretty/cute/etc every other day?" Drove him bananas, but he knew I was just teasing. Yes, of course it's a compliment.
FWIW, he now says "you look EVEN MORE NICE/PRETTY/CUTE/ETC today than every other day." I have trained him well.