The southern colonies had many different religions, but were primarily Anglicans or Baptists. The middle colonies also had many different religions, which included Catholics, Jews and Quakers.
The original laws of the colonies forced people to attend a kind of church and to also pay taxes that helped to pay for the churches. It was later that the colonists decided to become more religiously tolerant and to separate church from state. Interestingly, for all of its importance, the separation of church and state is not explicitly written into any of the founding laws, including the United States Constitution. The idea of the "separation of church and state" first appeared when Baptists in Virginia wanted to have religious tolerance from the Anglicans living in the area.