If Nintendo doesn't protect their IPs, they'll lose ownership of them.
So they say. The theory goes that, if a trademark holder doesn't enforce his trademark, it'll become generic, and if it becomes generic, they'll lose the trademark.
I don't see that happening anytime soon, especially not due to a port of a game.
To answer your question of "why are people mad", found in the larger context. People aren't mad because of this single instance in a vacuum. It's part of the larger debate about whether or not ROMs or emulators are ethical. Should we be able to take game that is no longer produced and make it playable with modern equipment? Should a game company be able to horde an IP away in the vault and allow nobody to enjoy it? Are either of those ethical?