Now the news has hit the BBC -
http://www.bbc.co.uk/news/technology-29204518Now even though I'm not a big fan of the whole Microsoft takeover idea, it sounds like they are keeping the majority of the Mojang Employees - which is a good start as they are the people that know the community as it s now, and know what to do in order to develop the game further.
Now we know funding was never an issue, but sometimes expertise is. I'm not saying the Mojang crew are not experienced, just look at the game they created and how popular it has been and continues to be! Microsoft may be able to help in that. Just look at the Halo series!
Plus Microsoft do have some very clever coders, so as has been mentioned on several websites, they might just be able to knock up a decent API to help Dev's make their mods.
At the end of the day - companies like Microsoft do eventually focus on profits. What we don't know about the deal is how much of Mojang's assets and rights to code / media are included in the deal. However, with one of their other popular games on the PC - Freelancer - they made sure the game was able to be modded. This led to many mod packs, of which some merged to be "must have" mods.
So, it would make sense for Microsoft to keep Minecraft free for Dev's to modify, and possibly even help them in some way (A good API for a start, and some way to stop mods conflicting with each other). Let's face it, the more awesome mods there are for a game, the more likely someone will show their friends, and the more likely their friends will want to get the game to play online with their mates, using those mods. Thus more sales.
Don't forget Realms - ideal for those people who don't want to play on a public server, but just with a few mates. Realms in itself is a monthly earner, and is far cheaper than running your own game server for the user. Imagine if Microsoft can port Realms to multiple platforms (and I'm sure they are already planning on it) - we could see the start of players on consoles hosting large worlds with a few select mods, and playing with people on PC, Mac, handhelds, etc at the same time - it's a big earner ... but it also develops the game