Hey! Do you mean 'Year of Wonders'? Anyways, Mompellion loses his faith because he realises that his devotion to Christianity was all in vain. So many people in Eyam died, those that are left resent him and ultimately he loses the one that he loved - Elinor. The 'wide green prison' he created was all because he believed that the plague was a 'trial from God' that could be conquered. Ultimately, however, nothing worked in his favour. That's why his 'hand is on the Bible, but he never opens it' and why he thinks 'God is a poor listener'. In becoming so committed to Christianity and taking such a literal interpretation of it, he contributed to not only his demise but of all those around him. He believes that he has failed in a position of authority.
(wow i wrote a lot lmao. hope that makes sense! legit just word vomit ahaha)