I have awful acne scarring that left my cheeks discolored and they look insanely awful in fluorescent lighting. My cheeks look all washed out flawed. Since fluorescent lighting is used practically everywhere, people never get to see the real me. Before you go saying how "guys are supposed to be rugged," well you haven't seen my awful cheeks which will turn any girl away (without proper lighting).
James Bond, Indiana Jones, The list goes on, every single one of those men that played those characters not judged harshly for wearing makeup on a daily basis. Why should you be? If it helps you become more confident it's worth it for that alone. Not to mention it'll help you weed out women that won't accept you for you, even if that means wearing makeup. Do what it takes to gain the confidence, and if a woman dares belittle you for wearing makeup, tell her to go a day without hers, see if she's game.
Go to a dermatologist, If you're only going to be wearing it up to cover you're cheeks. They might find you a permanent solution, and you won't spend time or money with makeup. Make up rubs off on clothes, on peoples faces sometimes. I only wear a little eye makeup, I went and got my skin fixed. Natural skin looks much better anyways.
If I knew a guy wore makeup I would think he is suspect to be honest. Are your cheeks really that bad though? No one is perfect, we all have flaws that we don't like but I don't know if the average girl would be turned off by your cheeks.
There's a difference between makeup for covering up blemishes and makeup for enhancing your look. If you're goal is to make your skin look normal then there's nothing wrong with that. If all you're doing is covering up acne scars then people shouldn't even be able to tell that you have makeup on so it shouldn't be an issue.