I think he's not so much against having Minecraft run on Windows 8 at all (i'm sure if Java support it, it'll run), I think he's just more averse to serving it via Microsoft's store.

I think Notch is overreacting in this case because he's already supported Microsoft's platform monopoly with Minecraft on the Xbox 360 (which is completely closed), so this stance seems kind of contrary.

Possibly there's some sort of clause in Microsoft's contracts that says an Application on the Windows Store can't be sold outside the store or something which he's actually getting up in arms about.

I'm not particularly crazy about Windows 8 either, but Notch probably needs to be a little more specific with his protests (then again, it is just a twitter post).