Basically I assume they just have a problem with TOO MUCH makeup, because yeah it makes you look totally different. I think they'd like to be able to recognize their girl without it :]
But there's really no problem with a little bit. Wearing a bit of makeup the right way just enhances your natural beauty, it doesn't change it. If you have just the right amount, they probably won't even really notice that you have any lol.
Yes they do at some point! Ever heard of a saying "what's underneath the mask?" well when a girl puts on makeup she's hiding her true beauty or sometimes her true unattractiveness! Some guys wanna wake up next to a woman seeing her not some kind of mask - same thing goes to dating one! Hope this helped!