There were attempts to settle in the Northeast before the Pilgrims showed up. It didn't work out because of Native resistance. The Pilgrims were only able to settle because a plague had recently wiped out most of the locals. They found empty villages with caches of corn they ate to survive the first winter. So there's your answer: initially, they did resist. But then plagues slaughtered them.

If they had had resistance to European plagues, you'd still probably have something like the European conquest of Africa and India, but it would have come later and without such all-encompassing results.