Introduction: the reign of Mary Tudor
It is said that the political change of the English Reformation took place in the reign of Henry VIII, and that the doctrinal one took place in the reign of Edward VI. However, after the death of Edward VI and the passing of the throne to 'Bloody' Mary I, England entered into a dark age so far as the reformers were concerned. Protestantism was outlawed, and the punishment for infringement of this law death by burning. 274 people were burned to death by Mary for the crime of worshipping God the way they believed best - Mary's sister, Elizabeth I, had no desire to repeat this affair. It had wrought much domestic unrest and was seen by Elizabeth as overly zealous - she is famous for saying she wished no window into men's souls, the unspoken collorary being that they were still expected to conform outwardly.
Mary had undone the work of her father in keeping with her true loyalties to the Pope and her strong Spanish Roman Catholic links. England had once again been placed in communion with Rome, and the Royal Supremacy which the able and political minds of Thomas Cromwell and Thomas Audley had secured was destroyed. Of course, none of this could be achieved without the approval of the Lords Spiritual and Temporal, but no Tudor monarch was allergic to interference in the affairs of Parliament, nor the appointment of Bishops amenable to their wishes in the sees of the nation.
So England was once again under heel of Rome, but the people liked it not. The disasters of Mary's reign only reinforced in their mind the evils of outside influence over their affairs, and the association of the strongly-Catholic Spanish and Mary's detested husband Philip II of Spain just made them associate Catholicism with unwanted interference even more so.
Elizabeth had been tutored by Protestants, and she never seriously considered maintaining Catholicism as the national religion. Denouncing Protestantism would have been disloyal to her parents, her friends, and her beliefs. The only question was how quickly she would seek to reimpose Protestantism, but this was a question requiring very serious consideration - Elizabeth needed to remain secure on her new throne, and Protestant leanings had the chance of aggravating the powerful Spanish.
Supremacy
The Act of Supremacy affirmed the sovereign's Supremacy over the National Church and removed all power from the Pope within English borders. The Queen was to be the final point of appeal for all members of the Church. One small piece of wrangling was required to get the Supremacy act through Parliament, however - Elizabeth was to take the title 'Supreme Governor of the Church of England', as opposed to 'Supreme Head.' This slight semantic wrangling appealed to Catholics who saw the Pope as the Head of the Church, and to Protestants who often did not believe any human could be the head of the Church, much less a woman. An example of this view is the speech given by Archbishop Heath on the Supremacy bill. He also speaks about the danger of England isolating itself on the international scene -
"First [say the reformers], we must forsake and flee from all general councils. Secondly, we must flee from all canonical and ecclesiastical laws of the Church of Christ. Third, from the judgement of all other Christian princes. Fourth and last, we must forsake and flee from the unity of Christ's Church. ... Her Highness, being a woman by birth and nature, is not qualified by God's word to feed the flock of Christ."
As well as this main point, it repealed Marian heresy laws, allowed Communion in Both Kinds, and established the Commision for Ecclesiastical Causes which was the civil authority used to correct error in the Church (the Queen and Privy Council were loathe to use it, however - they did not want to create an image of repression as had existed during the reign of Mary I.)
Elizabeth's view of the place of the Church within the state was that its authority stemmed from the monarch, but in a seperate stream to the civil authority. The Church had its own "Parliament" - called Convocation, which itself had both a Lower and Upper House. Elizabeth would have liked to push the religious changes through Convocation and banned Parliament from discussing matters of religion, but there were several reasons why she could not do so. One was precedent - Parliament had been spearheading religious reform since the time of her father, and were loathe to give up this privlidge now. The other was that there was a Catholic majority in Convocation that would doubtlessly have opposed what she chose to do. In reforming the system it was necessary to go outside of it, and while this strategy was fairly effective in passing the Act of Supremacy, things were not as easy in the case of the Act of Uniformity.
Uniformity
The 1559 Act of Uniformity was a strange beast, born of compromise - it fused into one the 1549 Act of Uniformity and the Book of Common Prayer from 1552. Some changes had to be made to the Book of Common Prayer to accomodate conservative members of the Queen's Council and parliament - ambiguities were left in which could have implied a belief in transubstantiation, if the reader wished them to. The reference to "the Bishop of Rome and all his detestable enormities" was removed.
Apart from the important Book of Common Prayer which defined Anglican beliefs, the other aspect of the Uniformity was enforcing outward conformity in the Church. This was important above all to Elizabeth, rather than any fundamental tenents of doctrine. So attendence of Church was enforced on the Sabbath and on Holy Days, with a fine payable to the poor relief funds if the law wasn't observed. Speaking out against the Book of Common Prayer or writing against it carried the punishment of a heavy fine or even imprisonment.
One of the things which was to enrage extreme Protestants but give them hope in the years to come was a line which stated that priestly vestments should be as they were in the second year of Edward VI's reign, until the Queen decrees otherwise. This was an expression of her control over adiaphora, which were things not related to salvation. Erasmians, who were hot on the idea of total religious freedom, saw this as an unwelcome intrusion by the state into Church affairs. No-one expected Elizabeth to enforce these rules, but the Vestiarian Controversy showed her doing so, albeit in a roundabout way.
The Lords passed the Uniformity bill only 21 to 18, and Elizabeth had imprisoned two Bishops because she suspected they would have voted against the bill. One was also mysteriously absent, and between them these three could have forced a draw in the Lords. The Commons had passed it easily.
Consolidation
These two Acts laid the groundwork for the English Church - a lot of the detail was filled in by Injunctions from the Queen and her Council. The first task was to administer the Oath of Allegience and deprive Marian bishops who were unwilling to conform. The number of deprivations was relatively little, perhaps as few as 200. This was done at a lazy pace, having been concluded by the end of 1559.
The next year, a set of Royal Commissioners were set lose on England and Wales to carry out a visitation. Their duties were mainly to administer the Oath of Allegiance to the lower clergy and carry word of the Royal Injunctions. These Injunctions filled in a lot of the detail of Anglican belief - a certain number of sermons were to be dedicated to the importance of the Royal Supremacy, there was a set diet of homilies, and shrines and images were to be removed. Altars were not to be desecrated, however. Although Elizabeth was making some concessions to the Protestants she enforced the use of wafer rather than bread in Communion, similar to the Roman Church.
In 1563, Convocation passed the Thirty-Nine Articles, which are still the official doctrine of the Church of England. This provided the theological grounding for the settlement along with the civil grounding provided by Parliament. Elizabeth was keen to keep Parliament out of religious matters as much as possible, and she blocked attempts for the Thirty-Nine Articles to be reviewed by the legislative branch of the civil authority.
The Queen-in-Parliament
While the evolution of Parliament during Tudor times is a subject for another node, it is important to note that Elizabeth's status in relation to Parliament and relation to the Church was different to her father's. Henry VIII had been granted the title of Supreme Head of the Church of England, which was a theological post, whereas as Supreme Governor Elizabeth held a secular post, approved by Parliament. In practice, this would mean little for Elizabeth because of her strong and assertive personality, but it could give room for wrangling in the future.
The Upper House had shown itself to not be afraid of resisting its monarch, but after this first parliament Elizabeth became a lot more conservative and less opposed to the interests of her governing class. Parliament could still not meet without the Monarch's approval, and the Queen was not adverse to coercion (such as the imprisonment of the Bishops mentioned above), but Parliament was becoming a much more dynamic and influencial part of the nation state.
Sources:
Alexander, H.G. Religion in England, 1558 - 1662: Hodder and Stoughton, 1968.
Graves, Michael A. R. Elizabethan Parliaments 1559-1601: Longman, 1987.
Lothingerton, John. The Counter-Reformation in Years of Renewal, 1470 - 1600, edited by John Lotherington: Hodder and Stoughton, 1988.
Saxon, Malcolm. Elizabeth I: Religion in The Tudor Years, edited by John Lotherington: Hodder and Stoughton, 1994.
Elton, G. R. England under the Tudors 2nd ed.: Cox & Wyman, 1974.