This question is not going to be answered properly. When girls ask this, guys imagine two girls who look about as hot, one with makeup, one without. Of course they prefer the one who is naturally pretty. Duh. That's like asking guys if they prefer natural 'c' cups or implant 'c' cups. Duh, natural. A more realistic question would be if they like natural 'a' or artificial 'c' (okay, for the record I prefer a cups anyway, but I think you see my point).
Most girls look better with makeup. If you don't look better, you're probably not putting it on properly. My wife knew a few excellent make up artists, one of whom used to be on TV quite often here. Trust me, any woman he puts make up on looks better, period.