Why did the pilgrims settle in the New England colonies?

They were looking for Religious freedom in the Virginia area and were blown off course.

The pilgrims and puritans were facing religious persecution in England. These religious groups left England hoping to find freedom to practice their religion,

That these groups settled in New England was a fortunate mistake. The Mayflower was damaged and blown off course in a storm. So the pilgrims landed in New England which was not their intended landfall.

It was a fortunate mistake because a small pox epidemic had emptied the land and villages in the area where the pilgrims landed. There was no immediate opposition to the pilgrims settling in New England.

A large tribe inland from the pilgrims landing had been weakened by the small pox disease. This tribe wanted to become allies with the pilgrims to strengthen themselves against incursions from other tribes.

The pilgrims felt that God had blessed their efforts to worship in their own manner by " arranging" the fortunate conditions in New England. Other groups of Pilgrims and Puritans followed the original group to New England.