Let's be honest. People who have any good reason to hate Mojang don't base it on the company alone. We've seen that through reading this thread. No, most people voice negative opinions on it because of the way the fanbase represents it. Let's break that down a little bit.
WARNING, WALL OF TEXT INCOMING. TL;DR AT THE BOTTOM.
1. Anyone who loves MineCraft will probably fight tooth and nail if the game was ever spoken badly of. Sometimes this is justified, specifically when baseless claims are made like "it looks stupid". That's not really based on any sort of fact. Other arguments made against MineCraft really hold water, and are quite compelling. "The game isn't a game, it's a toy," or "It's still in development," are among these. These are basically facts, not opinions, and MineCraft fans shouldn't try to argue against these claims. If someone dislikes the game, don't fight it. Offer reasons why you disagree, but don't tell anyone they're wrong. People see that and place a negative stigma on ALL MineCraft fans.
2. MineCraft should not have won MarchMadness. Let's be clear: I love MineCraft. It's just out of its league at the moment. It offers hours of entertainment, but it delivers a completely different experience from those offered by other developers. Their games are apples and oranges. Mojang shouldn't have even been entered in the competition, in my opinion. Yes, it got the game a LOT of publicity. But now, thanks to the blunders of a handful of individuals, there's now this underlying animosity between anyone who likes MineCraft and anyone who doesn't. If, say, the final round had been between BioWare and Valve, the outcome would probably leave the fans of each developer still being okay with each other. Obviously, preference in games isn't binary; there would have been lots of overlap and people who just couldn't decide on who to vote for. With Mojang it was different. Most people probably think it was unfair, since their fanbase is pretty rabid, and extensive. The votes weren't being given in spirit of the competition. Now all we're left with is a lot of angry glares between the two camps, with the occasional trollflame.
So where do we go from here? Mojang fans need to acknowledge that MineCraft can't be fairly called a full game yet. It should not be compared to other full-length AAA games head to head, even though the AAA industry can learn a lot from MineCraft's style. People need to relax and stop fighting over these petty differences. Sure, the other guy might not like MineCraft. Don't hate him for it! He's a human being, who just has different tastes and views than you. It's the same reason why people think all Christians are hypocrites. There's value in the things they represent, but they are poor representatives of those things.
TL;DR Version, MineCraft fans need to stop taking a binary view on games. Just because someone doesn't like what you like doesn't mean there's reason for personal attacks and trolling. Mojang isn't ready to be pitted against other developers or yet. MineCraft fans need to cool down and wait. Their day will come. Hopefully, in time, the fanbase's reputation will be improved.