If he didn't say he likes you better with makeup, that's something you're coming up with internally. Everyone looks better with makeup, you're not alone in that. Unless you get cosmetic surgery, fillers, botox, eyelash extensions, microbladed brows, etc you aren't going to just wake up looking amazing. And that's totally okay! I look exhausted without makeup.

It sounds as though you just would appreciate him being sweet with you even if you aren't all made up. Just talk to him about it and let him know you're feeling insecure. Unless you're dating an asshole, it's likely he didn't think about it and will try to make more of an effort if you tell him how you feel.