It's not because we look naturally worse without makeup, it's just because we're not used to it. Every single female in the media wears makeup and most girls who are considered 'really hot' by the public do wear makeup. Not all, of course.
However, I often see guys with really nice skin and notice that most girls who wear makeup often look washed out without it. Probably the makeup is damaging our skin somehow - it also blocks out the sun.