Thoughts on the Puritans continued... (for introduction, see "Who Were the Puritans?" Part 1 and Part 2)
“Canterbury fought with Rome in the days of Henry VIII and Edward VI and with Geneva in the days of Elizabeth….What made the second battle so acrimonious was that it was between foes in the same Protestant household.” So writes Horton Davies in Worship and Theology in England: From Cranmer to Hooker 1534-1603, and this is an accurate summation of the matter. The Puritans were convinced that the Church of England was “but hafly reformed.” They wanted to restore pure worship as they saw it in the Scriptures.
The Puritans’ Work Toward Reform
When it became evident that Elizabeth was not about to institute sweeping reform of worship in England, the Puritans set to work in Parliament and in parish churches. Fairly broad unanimity had been achieved doctrinally with the Thirty-Nine Articles (1563, 1571), but the practice of the church left much to be desired. Many parish ministers began to conduct public worship as they pleased. In the convocation of clergy in 1563, the Puritans set forward their desired reforms:
“…that at the celebration of the Lord's Supper the posture of kneeling, as suggesting the adoration of the elements, should be left indifferent; that the sign of the cross in baptism should be disused; that the wearing of copes and surplices be abolished, so that all ministers should use 'a grave and comely side (i.e., long) garment' or preaching gown; and that they should not be compelled to wear such caps and gowns as the Romish clergy.
“This overture not being approved, a motion was then brought forward to the effect that while Sundays and the special feasts associated with the events of our Saviour's life should be religiously observed, all other holidays should be abolished; that in all parish churches the minister in common prayer should turn his face to the people; that the cross in baptism be omitted; that kneeling at the sacrament be left to the discretion of the minister; and that it should suffice if he wear the surplice once, provided that no minister should say service or minister the sacraments but in comely garment or habit. After some discussion this motion was carried to the vote, when it appeared there was a majority in its favour by forty-three against thirty-five. But the proxies had then to be counted and these reversed the decision by one vote and only one, there being now fifty-eight for the motion and fifty-nine against. So that by the vote of one man, who was not present at the debate—that 'odd, shy man' as he has been called, it was thus determined to make no alteration in the ceremonies, and the Court party, therefore, carried their point in that memorable Convocation.”
The Puritans were stung by this defeat, but they were also emboldened by the knowledge that they had such widespread support. They continued their push for changes in worship. However, in 1566, Archbishop Matthew Parker laid out his “Advertisements” which reinforced the status quo.
The Puritans continued to work for change in Parliament, and their attacks zeroed in on the Book of Common Prayer. But in addition to this they began to publish and preach relentlessly. Not only did they put out polemical literature, they also published much devotional material, seeking to revive true religion in England from the ground up through families. The wealthier Puritan supporters endowed Emmanuel College at Cambridge University to keep a steady supply of well-trained Puritan pastors and teachers. They supported lectureships in various towns to disseminate sound doctrine. An entire network of “prophesyings” arose, which were meetings at which Puritan ministers would discuss the meaning and application of Scripture.
We now need to ask, “If the two factions were in broad doctrinal agreement, what differences in beliefs drove this struggle?”
Concepts of Scripture
Article Seven of the Thirty-Nine Articles, “Of the Sufficiency of the Scriptures for Salvation,” reads, “Holye Scripture conteyneth all thinges necessarie to saluation: so that whatsoeuer is not read therein, nor may be proued therby, is not to be required of anye man, that it shoulde be beleued as an article of the fayth, or be thought requisite as necessarie to saluation” (1572). The Puritans believed that the Church of England was not following this article to its true conclusion in its form of church order and worship. They believed that the Scripture governed more than simply doctrine and ethics. The Scripture provided the model by which the church should be structured. The church ought not to practice anything in worship which did not receive direct sanction from the Bible. The later influential Puritan theologian, William Ames, expressed it this way:
“All things necessary to salvation are contained in the Scriptures and also those things necessary for the instruction and edification of the church….Therefore, Scripture is not a partial but a perfect rule of faith and morals. And no observance can be continually and everywhere necessary in the church of God, on the basis of any tradition or other authority, unless it is contained in the Scriptures.”
The “Anglicans,” on the other hand, argued that God had indeed given us everything we need for salvation in the Scriptures. However, God has not given us everything that is to be done in church in particular. God was not concerned about the details, if you will, and he had left those to be determined by the wisdom gained from church tradition and right reason.
The Puritans thought this too convenient. It made it far too easy to set aside anything in the Bible which did not fit with contemporary practice. Instead, for the Puritans the Bible was the comprehensive word of God for all of life.
Concepts of Mankind
In addition to differences in their handling of Scripture, the two parties differed in their estimation of mankind. Although both believed in original sin, the Puritans held that the effects of original sin were much more pervasive than the Anglicans did. Thus, the Puritans tended to have a dim view of man’s reason, while the Anglicans had a more positive estimation. The Puritan William Perkins taught that original sin “is corruption engendered in our first conception, whereby every faculty of soul and body is prone and disposed to evil.” As Davies says, “If the Anglican apologist claimed that all God reveals must be comprehended by human reason, because the author of both revelation and reason is God, the Puritan replied that this was to make reason a judge over revelation, and man an arbiter of God.”
Concepts of the Church
While both Anglicans and Puritans believed in a national church, they differed over exactly what that meant. Puritans believed that the church comprised everyone in the kingdom; however, it was a mixed multitude. While all were baptized and thus members of the church, not all who were church members were actually converted. Furthermore, the Puritans sought to restore the church as it was practiced by the apostles. The Anglicans, on the other hand, did not agree that the Puritans were correct. They believed that the New Testament did not prescribe a once-for-all form of the church, and that with a Christian state there were important difference between the church in apostolic times and the church in Elizabethan England.
Concepts of the Sacraments
Both Anglicans and Puritans agreed on the basic nature of the sacraments as means of grace. They denied the Roman Catholic, Lutheran, and Zwinglian view of baptism and the Lord’s Supper. However, there was a noticeable difference in emphasis between the two groups. Anglicans saw the sacraments as primary channels of the knowledge and grace of God, but Puritans elevated preaching to this position. “In other words, for the Anglican the sacramental was the primary mode of Christ’s presence, but for the Puritan the primary mode of Christ’s presence was kerygmatic.”
 (Princeton: Princeton University Press, 1970), 40. I am indebted to Davies’ monumental study for the main structure of this post.
 John Brown, The English Puritans (Cambridge: Cambridge University Press, 1910). [Available online at http://www.monergism.com/thethreshold/sdg/brown/ brown_englishpuritan.html]
 The Marrow of Theology as cited by Davies, Theology and Worship in England, 52.
 The Golden Chain, reprint ed. (np: Puritan Reprints, 2010), 23.
 Worship and Theology in England, 56.