I never thought about it either, but it is totally something I would say too!
I think it depends on the situation and who it is coming from. I'd say compliment though.
Now once, I dressed up as an angel/devil for Halloween and had a co-worker tell me wow you look really pretty with make up on, and then stumble all over themselves to say I should wear it more often and oh not that I don't look pretty without it, etc... I thought I'd used a heavy hand for Halloween, as I don't wear much normally and had on fake eyelashes and tons of eye makeup and lipstick. LOL