Warren Keith Wright • Link
Though the term "fanatic" or "phanatique" was in use since 1525, by 1660 the word acquired new force to characterize (and denigrate) passionate nonconformists, both religious and political, especially the radical Puritan sects. The connotation broadened rapidly, and early in the 1661 Diary it will have become "a hostile epithet for all Nonconformists" (Companion, Large Glossary)---a heterogeneous assortment which would include Anabaptists, Fifth Monarchists (a millenarian sect), Quakers, and Presbyterians.
For one such as Pepys, who prized the traditions of the church he was brought up in, "fanatic" was a term of clear opprobrium. Later in the Diary he will discuss the strength of their numbers in London, how they were persecuted when it was feared they would foment civil unrest, and the vexed question of their true loyalty and patriotism. ("Shorter Pepys," index)