The MIB is Infected by BriarRose

So why does Jacob even care what the Monster thinks? Why does he bother to try and show the MIB that humanity has the ability to make the 'right' choices?

We don't yet know the nature of the "infection"---what causes it, what its ultimate effects are. "Being consumed by darkness" is kind of vague. We know it's powerful, and after Ab Aetorno, it seems pretty clear that Jacob isn't protecting the Island from the outside world---he's protecting the outside world from what's on the Island. I think that the MIB carries the infection, and Jacob is searching for a cure. By showing the MIB that humanity doesn't have to destroy itself---that people can choose to be good, that corruption can be fought---he's trying to give the MIB the tools to fight off the 'malevolence' and 'evil' that are consuming him. The Island isn't a prison, it's a mental hospital, and Jacob is the doctor desperate to save his patient's soul.

Maybe the MIB is the source of the infection. Maybe he's merely its end result---what Sayid and Claire will eventually become. But watching his rapport with Jacob makes it very clear that these two have a very strong bond. Jacob didn't bring the Others to the Island to protect it; he didn't bring them to fight the MIB. He brings people to the Island to show the MIB that he can be saved, and condemned himself to a similar eternity of imprisonment in the quest for the MIB's redemption.