The Protestant Reformation was a critical moment in European history which resulted in the desintigration of unified Christendom in the west. Keep in mind, Protestantism was of a fractured, fragmenting nature. There is not just one single Protestant Church; rather there emerged numerous Churches which could each give way to new disputes and conflicts, creating new Churches in turn.
This meant that Protestantism created a lot of social and political turmoil (the Early Moderns took religion very, very seriously). There was conflict between Protestants and Catholics as well as between different Protestant Churches. This history of conflict and division was critical in shaping the history of North American colonization.
When looking at the original Thirteen Colonies, in general, there are two major themes by which religion could influence the creation and growth of these colonies. On the one hand, a colony could serve as a proverbial "City on a Hill," governed according to its own religious doctrines. On the other hand, colonies could also be created as havens, where oppressed religious groups might find refuge. In both cases, the experience of the Protestant Reformation was key in shaping this history of colonization.