I'm with Holy Rapture on this one - I think people say "your makeup looks nice" because they wanted you to know that they noticed your makeup and think it looks great (like people compliment artists on their paintings/drawings/sculptures/whatever) and not because they think you're not pretty. They just want you to know that they've noticed something you've done that they think is really great.
The other thing might be that some people worry about saying "you look really pretty" when it's related to your makeup. I tell people things like, "I love that color you're wearing" or "Your eyes look so great!" because I don't want to just say "You look pretty" when I'm referencing someone's makeup, because I feel like you being pretty and your makeup being pretty are two different things, and while I compliment people on both, I have strong objections to people feeling like they're pretty because of their makeup or that they're not pretty without it, because I've never found that to be true. Ever since I was 13, I've been very sensitive to things like that because I've known people who felt like their makeup was the only pretty thing about them, and that they were, in a way, unacceptable if they didn't wear it. So I've tried never to reinforce the idea in anyone that they look pretty with makeup but not without it.
I'm also with Holy Rapture about your pic - if that's you, you are beautiful. Your makeup in the pic is quite nice, but you, all by yourself, are beautiful.