Perhaps the most immediate and significant effect the Restoration of Charles II had on religion was the re-establishment of the Anglican Church (also, the Church of England) as part of Charles II's attempts to eradicate all vestiges of the Commonwealth Interregnum, which included ridding the country of the Puritans.
Under an act known as the Clarendon Code, all religious non-conformity--the Puritans comprised the main body of non-conformists--was aggressively persecuted, in part because Charles II wanted to return England to the Anglican Church, and in part because the Puritan non-conformists were responsible for his father's (Charles I) execution. Whenever political and religious motivations mix, you can depend that the punishment of one group by another will be harsh.
Even though there were still pockets of dissenters--Quakers, Methodists,Baptists-- scattered around England after the Restoration, these people were persecuted socially and politically and, over a generation or so, their numbers declined. Later, religious non-conformists returned in droves, but for a hundred years after the restoration, non-conformists were significantly reduced.