With the Restoration of the Crown came the reimposition of the Church of England, and this showed another of the failures of the restoration; failure to address the religious issues released by the civil war and revolution.
There was no way the Church of England could represent England, nonconformity was still a definite reality no matter how many ministers were purged. The removal of the High Court of Commission also meant that the clergy were now less able enforce its will, and so ensuring conformity fell to the local governments, who in many cases sympathised with the religious radicals. Nonconformity was generally stronger within the cities.
Charles and Clarendon had actually hoped for a broader church than the one they ended up with, which consisted of divided Presbyterians and bishops who were not prepared to allow any kind of religious settlement. The Cavalier Parliament of 1661 furthered this, reimposing a more rigid church and ordering MPs to take communion by Anglican rite.
Though the public was completely against any toleration for Catholics, Charles was keen to try and achieve just that, and tried to introduce to repeal some laws against them – this failed. Yet Charles was not a religiously tolerant man generally – he fervently persecuted the Quakers, it was just Catholics situation which he tried to improve. This would have likely had something to do with his mother, wife and brother all being openly Catholic, and Charles probably was in secret.
Whenever there was a threat against the state from dissenters, Charles would introduce a repressive measure; such as the Conventicle Act in 1664 which was a reaction to the Northern Rising in 1663, and the Five Mile Act in 1665 which was a result of the Anglo-Dutch war. These made religious meetings of five or more people was forbidden, and the latter meant that any teacher or preacher who refused the Act of Uniformity could not go within five miles of any town or parish where they had taught. A second Conventicle Act in 1670 reinforced these further.
Despite the fact that Clarendon wanted a broader church settlement and opposed the measures that were taken, these became known as the Clarendon code.
The English Civil War (And Its Long-Term Effects) 