Well, I'm not him so no way would I be 100% I know what was in his mind, but I can guess. He probably thinks you're cute every day, and today he got the opportunity/courage to tell you. You're beautiful with or without the makeup, he's probably flirting with you, didn't notice that you hadn't done your hair and makeup (let's be honest most guys are oblivious), or he noticed you didn't, but is still very much attracted to you, perhaps even more so.

some guys (back in my day) prefer a more natural look.

or (and this is legit) some guys are intimidated when a woman looks too good. the term "out of my league" comes to mind.

and the fact that you think he's cute? well cute people have insecurities too

Maybe he likes the "natural" look better.
I know that I do.

You probably put on too much make up and look fresh when you’re without them.

I think you should just accept the fact that you look good

May be you have mindset that makeups only makes you beautiful 😀.

He likes the natural look

Maybe he enjoys the feral look

sorry but... wasn't he simply joking?

Heh in my experience when a woman thinks she doesn't look great "hot garbage" is usually their description. They look ten times better than they think. I always have thought hair with a little "messy" like as in kinda tussled around a bit. Usually looks ridiculously hot. It was a compliment if nothing else..:) maybe he will be checking you out from now on to see if you look that way again. ;)

That's hot.

I always look like “trash” and some guys prefer women who don’t put so much effort into their appearance.

You're overthinking it.
It could really just be an honest compliance.