I mean, it's fine that you feel this way, but I honestly don't understand what is baffling to you about people who don't wear make up. I wear make up sometimes, but not everyday and not when just at home.
Why wouldn't you want to look the best you can all the time?
It's subjective. I like my face. Sure, with make up I look "better" by the beauty standards of our time. But why on earth should I care about that? My face isn't so hideous that it needs to be covered all of the time least someone be forced to endure its natural awfulness.
And anyway, I'll wager any money that you don't look the best you can all the time. Sure you wear make up, but you won't have perfect hair, your very best clothes, your maximum amount of sleep, every single day. So actually you do understand why people don't look their best all the time.
I have a friend in her 60s and if we go out she wears lipstick and mascara and looks 20 years younger!
Why would I want to appear younger than I am? I have no interest in befriending people who would look down on me for being my actual age. So there is no benefit to appearing 20 years younger.
I also would wear make up if I'm just at home hanging out with my DP...I want to look my best for him. I find it baffling that people will do their hair and make up to go out with with work colleagues but don't do the same on a daily basis for their partner...
I don't want to look my best "for" my partner. I am the way that I am. If he's not into it, he can go elsewhere. My partner values me for much more than the colour and lengh of my eyelashes, thank the lord.
The reason I wear make up at work and not at home is that work is a competitive environment. I want to look more awake and with it, and I know that some people (like you) look down on other women's natural faces.