That's a good question. If I were in ur shoes, and it was my girlfriend, I'd tell her " why do u cover ur beautiful face with that stuff? I fell inlove with u.. Not ur make up. Besides you don't have to try to impress me. Touch already got me" my woman just uses eye liner. But if she did wear make up, this is what I'd tell her :-) let me know how it works out man.
If you want to do it without hurting her feelings wait until the next opportunity comes up when she has little or less on. After swimming etc. You could say " I love how pretty you look, I never realized how pretty your eyes look, the liner hides them..." Something like that, when she is wearing little or less might go over better.
Honey, I think you're gorgeous AND I really think you look naturally beautiful with less make up, will you wear less for me so I can admire your good looks. Just remember to say "and" instead of "but" because the word but cancels out everything that came before it.