Personally, I use Windows because I like it, it works, and I know how to use it well. Why would I potentially waste my time trying to migrate to another operating system when I have one that works for literally everything I need? While Microsoft is by no means perfect, I find them to be very preferable to Apple or...whoever works on whatever flavour of Linux I'd install if I became the victim of massive head trauma.
Also, I'm not sure if its been said in the past few pages or not, I can't really be bothered to look too deep, but I know exactly why Microsoft wants Minecraft, and its nothing at all nefarious. The game itself was just an incidental acquisition, what they're after is the merch. Keychains, plushies, foam swords and picks, hoodies, decorative beer steins, and the like. I'd be wholly unsurprised if merch constituted around two thirds of Mojang's profits from Minecraft. That's what happens when a game becomes popular: it stops being just a game and becomes a culture. Cultures are profitable in the extreme. Look at things like My Little Pony, Transformers, and Dragon Ball Z. Those things are more than just their respective shows, they have an entire culture built around them, and culture means merchandising. Microsoft could care less about the game, what I've read has indicated such. They didn't mention modding directly not because they have some sinister, nefarious ulterior motive, but simply because they don't care about it. If anything, it means free advertising for them, and even more merch sales. Microsoft is many things, but not a one of them is incompetent.