I think Ultimate MJ came closest to the answer I wanted to hear.
Heroes and Villians were infected first. And since they knew how to battle, ordinary people became food. They weren't allowed to become fellow zombies.
Magneto, because of his powers, was able to evade them for a long time. If they had not torn him apart so quickly, he would have come back, too.
About the Ultimate Dr. Doom, I think he probably fought with the Zombies for a while, realized it was a stalemate and performed some magic to move himself to a safe place, probably off-planet.