If they have a solid idea of how they want to use the IP, it makes sense. It also comes with a massive risk though - it will be very easy for them to "be the guys who ruined Minecraft".
I imagine it will need to be something like "stay very hands-off for a significant amount of time to prove that they didnt in fact ruin it" followed by some way of turning it into a link in and value add for their existing products rather than something that they sell expansions/new stand-alones for.
Something like Minecraft being the Tetris/Solitaire of the 2010s or so? It comes pre-loaded with their OS's, create a great experience on surface tablets etc, trying to turn it into "the new Microsoft gives you cool stuff and makes it open for everyone" to position Microsoft as the open alternative to the more closed environments of Google and Apple?
I dont see how the purchase makes sense from a money-making point of view today - the Mojang crew hasn't proven they can do repeated success with new IPs, but I could totally see it making sense from a holistic point of view - successful integration of Minecraft in the Microsoft universe could add significant value to Microsoft as a whole.