Notch isn't developing, but it's ultimately his IP. He's made over $100M in licensing deals on the brand alone. I'm sure he's going to be the shotcaller (if not just a providing a massive influence) for any large-scale potential deals involving it.
Even with that aside, he's a massive figure in the game development community. A lot of people respect him and look up to him for making out huge in the Indie game in industry pretty much of his own accord. His opinion is pivotal.
Yes, Jeb seems to be the technical lead on Minecraft these days.
But I believe that Notch and his partners still make all the calls for the company at large. While his declaration seems a bit brusque, I think the Mojang guys have quite a bit of pride in being an independent company that has done well and may wish to clearly make their corporate philosophy known.