See Agnosticism http://www.pepysdiary.com/encyclopedia/1685/
Per JonTom Kittredge on Fri 20 Jan 2006 http://www.pepysdiary.com/diary/1663/01/18/#c40810
Atheism and Agnosticism
I’m not sure that Christianity was quite so unquestioned as that.
From 15 May 1660 ( http://www.pepysdiary.com/diary/1660/05/15/ ): “In the afternoon my Lord and I walked together in the coach two hours, talking together upon all sorts of discourse: as religion, wherein he is, I perceive, wholly sceptical”
That sounds to me like agnosticism, at the most. Granted Sandwich is only stating this in private; doubtless it would have been dangerous to espouse it publicly. I’m just saying that some people did think this way, and did talk about it with their friends.
My own view is that Pepys was brought up in an age of great piety. He seems to have subscribed, or at least acceded to, the conventional religion of his time. But I don’t see any evidence that faith meant much to him personally. His invocations of God seem to me to be reflexive rather than deeply felt. The ’60s seem to have been a time of reaction against the religious enthusiasm during the Commonwealth. I got the sense that religion mattered more to Sam at time he began the diary than it does “now.” [i.e. three years on, Jan. 1662/63]