They have, but they've also been helped by the former center of Mojang's fanbase's cult-of-personality going completely off the deep end. If Notch was still "that quirky dude making little games here and there" instead of a chud screaming on Twitter all the time, I tend to think there would be more (unreasonable, but extant) dissatisfaction with Microsoft's handling of Minecraft.

Oh yeah, I totally forgot. Their handling of Minecraft has been mostly great, from both a product and software quality perspective. (except for the modding stuff)