It's helpful to understand the history of why prayer books were instituted in the first Reformation. It was basically a crutch. It was understood that many of the clergy who had until that point been saying mass had no idea how to pray or preach in a biblical way, or administer the sacraments, and yet, somehow, protestant services had to immediately take place throughout whole kingdoms, so they would give them a book of prayers and homilies to help them.
There is some evidence from the period that it was viewed this way. For example, the Scots had a book of common prayers from their sojourn in Geneva, but in the First Book of Discipline (1560), they recommend ministers be able to pray and preach, and the only reference to the common prayers is for readers, which was the office of those preparing for ministry and perhaps not yet able to pray and preach well. It says the following:
"To the Churches where no ministers can be had presently, must be appointed the most apt men that distinctly can read the common prayers and the Scriptures, to exercise both themselves and the Church, till they grow to greater perfection, and in process of time, he that is but a reader, may attain to a farther degree, and by consent of the Church, and discrete ministers, may be permitted to minister the sacraments..."
Now, with the passage of time, the church was able to ordain more qualified, well-educated ministers, who were able to preach and pray without using set forms. And so we can imagine how it would have been taken, in 1637, after almost 80 years of reformation, at a time when all ministers were properly trained for the ministry and experienced in prayer and preaching, that the bishops would order ministers not to pray any prayer but what was found in the prayer book. That, combined with the Scots not recognizing the authority of the bishops to begin with, led to this being viewed as an unprecedented act of ecclesiastical tyranny. Can we imagine, in our churches today, if a foreigner power showed up and told us that the pastor can't pray any more, unless he does so out of the book of prayers they approved? I don't think that would go over well.
The directory for public worship (1645) actually addresses the reasons for doing away with the prayer book in the preface. It says,
"IN the beginning of the blessed Reformation, our wise and pious ancestors took care to set forth an order for redress of many things, which they then, by the word, discovered to be vain erroneous, superstitious, and idolatrous, in the publick worship of God. This occasioned many godly and learned men to rejoice much in the Book of Common Prayer, at that time set forth; because the mass, and the rest of the Latin service being removed, the publick worship was celebrated in our own tongue: many of the common people also receive benefit by hearing the scriptures read in their own language, which formerly were unto them as a book that is sealed.
Howbeit, long and sad experience hath made it manifest, that the Liturgy used in the Church of England, (notwithstanding all the pains and religious intentions of the Compilers of it,) hath proved an offence, not only to many of the godly at home, but also to the reformed Churches abroad. For, not to speak of urging the reading of all the prayers, which very greatly increased the burden of it, the many unprofitable and burdensome ceremonies contained in it have occasioned much mischief, as well by disquieting the consciences of many godly ministers and people, who could not yield unto them, as by depriving them of the ordinances of God, which they might not enjoy without conforming or subscribing to those ceremonies. Sundry good Christians have been, by means thereof, kept from the Lord’s table; and divers able and faithful ministers debarred from the exercise of their ministry, (to the endangering of many thousand souls, in a time of such scarcity of faithful pastors,) and spoiled of their livelihood, to the undoing of them and their families. Prelates, and their faction, have laboured to raise the estimation of it to such a height, as if there were no other worship, or way of worship of God, amongst us, but only the Service-book; to the great hinderance of the preaching of the word, and (in some places, especially of late) to the justling of it out as unnecessary, or at best, as far inferior to the reading of common prayer; which was made no better than an idol by many ignorant and superstitious people, who, pleasing themselves in their presence at that service, and their lip-labour in bearing a part in it, have thereby hardened themselves in their ignorance and carelessness of saving knowledge and true piety.
In the meantime, Papists boasted that the book was a compliance with them in a great part of their service; and so were not a little confirmed in their superstition and idolatry, expecting rather our return to them, than endeavouring the reformation of themselves: in which expectation they were of late very much encouraged, when, upon the pretended warrantableness of imposing of the former ceremonies, new ones were daily obtruded upon the Church.
Add hereunto, (which was not foreseen, but since have come to pass,) that the Liturgy hath been a great means, as on the one hand to make and increase an idle and unedifying ministry, which contented itself with set forms made to their hands by others, without putting forth themselves to exercise the gift of prayer, with which our Lord Jesus Christ pleaseth to furnish all his servants whom he calls to that office: so, on the other side, it hath been (and ever would be, if continued) a matter of endless strife and contention in the Church, and a snare both to many godly and faithful ministers, who have been persecuted and silenced upon that occasion, and to others of hopeful parts, many of which have been, and more still would be, diverted from all thoughts of the ministry to other studies; especially in these latter times, wherein God vouchsafeth to his people more and better means for the discovery of error and superstition, and for attaining of knowledge in the mysteries of godliness, and gifts in preaching and prayer.
Upon these, and many the like weighty considerations in reference to the whole book in general, and because of divers particulars contained in it; not from any love to novelty, or intention to disparage our first reformers, (of whom we are persuaded, that, were they now alive, they would join with us in this work, and whom we acknowledge as excellent instruments, raised by God, to begin the purging and building of his house, and desire they may be had of us and posterity in everlasting remembrance, with thankfulness and honour,) but that we may in some measure answer the gracious providence of God, which at this time calleth upon us for further reformation, and may satisfy our own consciences, and answer the expectation of other reformed churches, and the desires of many of the godly among ourselves, and withal give some publick testimony of our endeavours for uniformity in divine worship, which we have promised in our Solemn League and Covenant; we have, after earnest and frequent calling upon the name of God, and after much consultation, not with flesh and blood, but with his holy word, resolved to lay aside the former Liturgy, with the many rites and ceremonies formerly used in the worship of God; and have agreed upon this following Directory for all the parts of publick worship, at ordinary and extraordinary times. Wherein our care hath been to hold forth such things as are of divine institution in every ordinance; and other things we have endeavoured to set forth according to the rules of Christian prudence, agreeable to the general rules of the word of God; our meaning therein being only, that the general heads, the sense and scope of the prayers, and other parts of publick worship, being known to all, there may be a consent of all the churches in those things that contain the substance of the service and worship of God; and the ministers may be hereby directed, in their administrations, to keep like soundness in doctrine and prayer, and may, if need be, have some help and furniture, and yet so as they become not hereby slothful and negligent in stirring up the gifts of Christ in them; but that each one, by meditation, by taking heed to himself, and the flock of God committed to him, and by wise observing the ways of Divine Providence, may be careful to furnish his heart and tongue with further or other materials of prayer and exhortation, as shall be needful upon all occasions."