I have no thoughts on the matter myself. Yogscast may be entitled idiots (after all, not the first time fame have gotten too much for anyone), or there may be an misunderstanding or something.
What I don't like is the escalation the fanboys (on all sides) makes it. They do make it a lot worse (after all, I don't think the first, or the second, tweet is especially inflaming.)
Notch shouldn't have said anything at all of course, but I do get the feeling that he had to apologize (and he didn't say who they were in that first tweet, he just apologized and the co-founder of the company agreed on that tweet). And then the "fans" have to inflame everything.
I must admit I would really laugh if everything just was a big troll (from both sides) for the next "Shadow of Israphel" where Notch (the real Notch) turns out to be the big bad or something. It's quite strange that Yogscast have to make a video response after all, and have to have several days to make it.