Cuban has ranted about software patents publicly many times. He's just putting his money where his mouth is. Even if he's done little that's innovative (I don't know, I'm not especially familiar with his history), there's no reason he can't still be opposed to software patents.

This is irrelevant to whether they are allowed to support the EFF or not.

Well, Minecraft is the one of the largest (if not the largest) indie developed game in the world. So there's that.

biggest != technical innovation

Quake 1 had better graphics and editors eons ago