There was no single denomination or religion in the Middle Colonies. Instead, they were home to members of a number of different Christian sects. Some of the first colonists in the region were Swedish and Dutch Lutherans. William Penn, the founder of Pennsylvania, was a Quaker and granted full religious freedom in his colony.
This religious tolerance attracted colonists of many denominations to the region. As a result, many Catholics, Calvinists, Mennonites, Presbyterians, and German Baptists came to settle in the Middle Colonies. French Huguenots fleeing persecution in France also came there to freely practice their religion in safety. Even a small population of Portuguese Jews settled in the Middle Colonies. There was also a significant Anglican population as this was still the official church of England.
This diverse population of members of different religions characterized the Middle Colonies as being more accepting of religious differences than elsewhere in British North America. If you compare this to the staunchly Puritan New England colonies (excepting Rhode Island) or Virginia which required its colonists to attend Anglican services, you can see that religious pluralism was one of the defining characteristics of the Middle Colonies.