I can see your point when it comes to bolder makeup stykes, but faux-natural makeup will do wonders for pretty much any woman. I wear my makeup far more natural looking than many women yet I definitely look different without it on. Not in a completely-different-woman way, but I have dark spots, lack eyebrows, and very unnoticeable eyes. Light, "natural" makeup makes me look like I have the perfectly clear skin of a child, a normal amount of eyebrows, and eyes that pop.
I'm rather sure that in general, a man in his right mind would prefer me with my light amount of makeup on, just because the makeup helps the features I already have stand out in a basic, universally attractive way. I personally don't care for makeup, but I know it makes me look better, so I put it on every day.
However, there are many women who genuinely love wearing makeup! It can be like art---you feel a sense of accomplishment when you're done, knowing that you got your eyeliner wing just right or arched your eyebrows perfectly. Most guys DONT care if a girls makeup is "on fleek" or not (I dare say most prefer women whose makeup isn't, considering the current "on fleek" look is very bold and fake looking), but women who are truly into makeup don't give two craps about men's opinion of it, so there's that.
The of course you have the women who use makeup to compete with other women. They want to look amazing according to other WOMEN'S standards---standards that are very different from men's, I might add. Currently, blending 20 butt loads of foundation on your face, drawing on ultra arched, perfectly symmetrical eyebrows, and adding dramatic false eyelashes is all the rage in woman-land, and women who do their makeup like that are bound to get plenty of compliments from other women. Men? Not so much. But that is irrelevant because the competition is with other WOMEN.
So basically, the issue of makeup is too multifaceted for your simple "why do women wear makeup if us men don't even like it" question, primarily because that's being asked under the assumptions that not only is all makeup unappealingly noticeable, but also that all women wear makeup to attract men in the first place.