The Puritans didn't think that the Church of England was sufficiently Protestant in its doctrines and practices. Puritans were Calvinists and looked to Calvin's Geneva as the model for the kind of theocracy they wished to see established in England. But the Church of England, especially after the Elizabethan settlement of 1559, was always something of a compromise between different factions. This was thought to be the only way to maintain peace in a kingdom fractured for decades by bitter religious conflict.

But the Puritans weren't satisfied with this compromise; they believed that the Elizabethan settlement retained too many of the old Catholic elements. In particular, some of the more radical elements among the Puritans railed against an episcopal form of church government, that is to say a Church formed on a hierarchy of bishops. Many Puritans wanted a much simpler, less hierarchical form of church government, with much less visible pomp. However, Queen Elizabeth I fiercely resisted any such proposals. As far as she was concerned, an episcopal form of government was an essential part of a society ruled from the top down. If the bishops could be got rid of, then the same principle behind Puritan church reform could just as easily be applied to the social order as a whole, undermining the power of society's traditional rulers.

The Puritans wanted to change or "purify" the Church of England.  Though the Church of England was established to be separate from the Roman Catholic Church, it still resembled it in many ways.  The Puritans disagreed with this.  They were against doctrine and liturgy that originated in the Roman Catholic Church and yet remained in the Church of England.  The Puritans wanted to look to the Bible for church doctrine, rather than to the traditions of Catholicism.  They wanted the Bible alone to be their source and guide in matters of the church.  They felt that this would be a way of truly separating from the Roman Catholic Church.  

While some considered Puritans to be judgmental and close-minded, their movement grew in England.  In addition to changes in the Church, Puritans also believed in living a lifestyle based on Biblical principals.  They believed in keeping the Sabbath and behaving in a manner which honored God.