I think it really depends on multiple factors, but I feel like tl;dr putting player made content in the game (with permission of course) is like a swamp for potential legal issues. I'll explain below:
So imagine you are an indie developer with a smaller team (not Mojang basically lol). Someone made a really cool mod for your game and you want to ask if you can use it in the base game. You can ask for permission and they say yes, cool! But what if two months down the line they decide for whatever reason they don't want this anymore? Then you'll end up removing it, causing your fanbase to be upset if someone did like it and so on... basically this is very far from ideal. What if they sign a contract? That would be better but it's not 100% guaranteed to forever be part of the base game now.
Then imagine you're a big company. Dealing with the above legal issues may be a little bit easier, but putting such a big risk on cutting content from the game can cause a reaction from the audience that is far from favorable. They'd rather do things with their own team to avoid any kind of trouble and keep their company name and reputation clean.
So in the end I just think that a lot of different things can contribute to not including mods, but in general, you avoid a lot of potential issues with cutting content and just upsetting fans by not putting user content into the base game. I think it's really cool to see mods make it to base game though, and I've seen it happen with a few games before, so it really just depends on the risks you want to take and how careful you are about them! :)