Interesting Question! :)
While a girl's make-up does really capture a man's attention at first sight, over time it is what a girls personality and attitude which will matter to most guys.
Men want women who are confident, content and strong enough to face her flaws. A woman who has no make-up on most often than not exudes these three characteristics eclipsing their physical appearances.
Another reason is that girls fully-covered in make-up makes them look like high maintenance which makes most men think that they are way above their level.