Jacob obviously seems protective about the island, but maybe only to the extent that he is highly selective about who he wants to bring there. However, he does bring people. LOTS of people, it would appear.
In The Incident, MiB seems dubious about the ship coming to the island: "They come. They fight. They destroy. They corrupt. It always ends the same." It's MiB who doesn't want people on the island. This takes place when MiB was in his original human form, during the (pre-Steinbeck) 1800s.
How did the Black Rock end up in the middle of the island? Right after that conversation, MiB marches over to some special place on the island where there's another device that can move the island--say, a Warm Kingston Valve. However, instead of moving the island horizontally, the WKV moves the island vertically. Unfortunately for MiB, he wasn't able to sink the island for very long, but still suffered the consequence of activating the WKV--turning into a lethal pillar of black smoke.
MiB has found whatever loophole he needed, and set into motion a series events which he hopes will cause the island to sink for good.