The problem with the Reformation was that it succeeded because it was supported politically. Gospel Christians had no freedom under Rome & were suffered accordingly. Hoped for freedom through the Reformation did not occur because the Reformed churches allied with the new "powers that be."
That situation continues throughout the world, under atheism, communism, Islam, Hinduism & all other religions, including modern Christianity increasingly.
The religion-state links continue to oppress, as seen in Acts 4, & under Catholicism with the "conversion" of Constantine & suppression of the Donatists who refused to conform. Baptism of anyone "baptised" by the Catholic church became a capital offence.
Gospel Christians should be free under any & every secular power. The problem occurs when state & religion act together, so that non-conformists & supposed heretics are seen as rebels.
The Westminster Confession declares:
23:III. (The civil magistrate may not assume to himself the administration of the Word and sacraments, or the power of the keys of the kingdom of heaven: yet he hath authority, and it is his duty, to take order, that unity and peace be preserved in the Church, that the truth of God be kept pure and entire; that all blasphemies and heresies be suppressed, all corruptions and abuses in worship and discipline prevented or reformed; and all the ordinances of God duly settled, administered, and observed. For the better effecting whereof, he hath power to call synods, to be present at them, and to provide, that whatsoever is transacted in them be according to the mind of God.
The Congregational/Independent Savoy Declaration reads:
24:3 Although the magistrate is bound to encourage, promote, and protect the professors and profession of the gospel, and to manage and order civil administrations in a due subserviency to the interest of Christ in the world, and to that end to take care that men of corrupt minds and conversations do not licentiously publish and divulge blasphemy and errors, in their own nature subverting the faith and inevitably destroying the souls of them that receive them: yet in such differences about the doctrines of the gospel, or ways of the worship of God, as may befall men exercising a good conscience, manifesting it in their conversation, and holding the foundation, not disturbing others in their ways or worship that differ from them; there is no warrant for the magistrate under the gospel to abridge them of their liberty.
The 1689 Baptist confession has no corresponding clause, simply expecting:
24:3. Civil magistrates being set up by God for the ends aforesaid; subjection, in all lawful things commanded by them, ought to be yielded by us in the Lord, not only for wrath, but for conscience sake; and we ought to make supplications and prayers for kings and all that are in authority, that under them we may live a quiet and peaceable life, in all godliness and honesty