The other side of the story is that notch contacted Microsoft about the sale in the first place, and he was pretty transparent about the reason why, after it was done: http://notch.net/2014/09/im-leaving-mojang/
Notch didn't contact Microsoft, they contacted him.
“Anyone want to buy my share of Mojang so I can move on with my life?” he asked. “Getting hate for trying to do the right thing is not my gig.”
"Mojang CEO Carl Manneh was sitting at home with his family when he first saw the tweet. Within 30 seconds of his reading it, his phone rang. A Microsoft executive who coordinated with Mojang wanted to know if Persson was serious. “I’m not sure–let me talk to him,” said Manneh.
"While Persson originally wrote the message as a half-joke, the realization that he could disassociate from Mojang took hold. The man who once publicly pledged that he would not sell out to evil corporations now had his head turned.
"In the week that followed, Manneh’s phone rang constantly with interest from Microsoft, Electronic Arts, Activision Blizzard and others. Talks with Activision petered out. Persson, cryptically, won’t discuss what happened with EA but says that Mojang ruled out potential buyers “who did game play in a way we didn’t like.” Microsoft, however, apparently passed muster."
Oh, right, I could've sworn it was the other way around, sorry for the confusion.
Either way, it was pretty clear he wanted out, with what I think are valid reasons. The article makes it look like a "take a money and run", leaving a dissatisfied bunch of employees behind.
First, the employees seemed dissatisfied before (why that is relevant to the sale, I am not sure), and it seems to me the deal was pretty good for them.
Second, and this is just my impression, is that Minecraft, from the community's PoV was already completely outside the hands of Mojang's founders, so they didn't exactly abandon the product.
Ah, I had forgotten about this posting when I posted my earlier comment. He says flat out that it's gotten too big for him to deal with and that it's not fun anymore.
It's kinda the double edged sword of making something awesome- on the one hand, you've made something awesome. On the other hand, now you're in charge of your awesome thing that's way too big for one person to handle alone, so the bigger it gets the more people you have to bring in to run it, and the further and further away from being directly involved in the day to day. Unless you're Steve Jobs, but not everyone can be or wants to be that way.