From Historical England

English persecution under the reign of Elizabeth, however, did not confine itself solely to the Catholics.  The Puritans also felt the heavy hand of the state.  John Whitgift, her minister in the Canterbury see, subjected Puritan preachers who refused to support the state religion to such intense religious inquiry that it was compared to the Spanish Inquisition.

While King James I attempted to reconcile the religious division within his government, persecution resumed again under King Charles I.   As an example, one woman who insisted on keeping Saturday as the Sabbath was imprisoned for 11 years.  In fact, it was continued religious tension between the Puritans and the established church that led to the revolution in the mid-17th century, which ultimately ended in the execution of Charles I.

When this new Puritan government achieved power under Oliver Cromwell, Scotland revolted, fearing an establishment of the Puritan religion in their lands (they had previously established the Presbyterian faith).  Scotland declared Charles II to be the rightful King, and forced him to "maintain or establish" Presbyterianism in all of his lands.  The rebellion was eventually crushed under Cromwell's military leadership.

Cromwell himself believed in the importance of an established state religion. Puritans, Baptists, and Presybeterians had the official sanciton of the state. Anglican pastors, previously favored by the state, were forced to minister to their congregations in secret.  The same held true of Roman Catholic priests. In 1657, Parliament passed a law stating that anyone over the age of 16 who did not disavow Catholicism would forfeit two-thirds of his property.  No better words can be found to describe this time period than Durant's:  "Intolerance was inverted rather than lessened.  Instead of Anglicans persecuting Catholics, Dissenters, and Puritans, the triumphant Puritans, who formerly had clamored for toleration, now persecuted Catholics, Dissenters, and Anglicans."

After the Restoration, King Charles II attempted to implement a program of religious toleration, which was met with hostility from all Christian sects.  Parliament, which was now predominantly Anglican, restored ecclesiastical courts to punish those who didn't pay tithes to the Anglican church.  The "Corporation Act" allowed only people who had taken the sacrament according to the Anglican rite to hold public office.  The "Act of Uniformity" required all pastors to agree with the Book of Common Prayer. Quakers and Puritans alike now became the subject of state persecution.

Charles II opposed Parliament's extremism, and in 1672 issued a "Declaration of Indulgence for Tedner Consciences."  It was essentially an edict of toleration towards people of dissenting faiths.  It was as a result of this proclamation that the great Puritan John Bunyan (the author of "The Pilgrim's Progress") was freed from jail.

Under pressure from Louis XIV, however, Charles annulled this declaration in less than a year. Parliament continued in its effort to remove dissension from the ranks.  The "Test Act" was passed, requiring all office holders to solemnly reject the Roman Catholic doctrine of transubstantiation, and, once again, to take the Sacrament according to the prescribed Anglican rite.

In 1678, the "Popish Plot" reign of terror began.  It was feared by Protestant England that the Pope, together with Louis XIV, the Archbishop of Armagh, and a selection of Jesuits, had initiated a conspiracy in which King Charles II would be killed and his Catholic brother would ascend to the throne.  The ensuing mayhem was typical of the usual historical examples of state-sponsored fear-mongering:  false witnesses were drummed up, people (especially Catholics) were guilty until proven innocent, and many were sent to a premature death. 

From Historical France

Louis XIV, arguably France's greatest king, also took measures to further the agenda of the state religion of Roman Catholicism.  In the mid-17th century, he instituted a series of measures which revoked The Edict of Nantes (which promoted religious toleration).  He completely outlawed Protestant worship in the Gex province.  When children came of age, they were forced to either accept conversion to Roman Catholicism or leave their parents.  The Huguenots were barred from establishing new schools, as well as from emigrating.  Some 500-600 of the Huguenot churches were closed.  Some were torn down.  Those who tried to worship amongst the remnants of their old churches were punished as enemies of the state.

On October 17, 1685, King Louis XIV completely revoked the Edict of Nantes. Huguenot worship and teaching was outlawed.  Their pastors were ordered to leave France (although other Huguenots were still forbidden to leave).  All children born in France were required to be baptized by a Roman Catholic priest.  Huguenots outside of Paris were subject to "dragonnades."  According to one authority, soldiers made the Protestants dance until they were exhausted, they poured boiling water down their throats, they pulled hair out of their beards, they beat them, they burned their arms and legs with candles, they forced them to hold burning charcoal in their hands, and committed other such atrocities against them.  It has been referred to as the holy terror of 1685.