I was hoping to find a book that was:

a) historical fiction

b) explained the move by people from Catholicism to other religions

c) I've enjoyed Phillipa Gregory's, The Other Boleyn Girl, explanation of the break from Catholicism to the Church of England

d) Are there similar books that explain the shift to Presbyterianism and Protestantism?

Hmm...good question! I think one of the Cynthia Harrod-Eagles books deals with the rise of Protestantism, maybe the one titled "The Princeling".

I looked it up and The Princeling is about a "Catholic family and the challenges they face as England becomes a Protestant country". Maybe not really what you are looking for.

You might want to check out this site - http://www.historicalnovels.info/index.html

You can search for the correct time period and do searches for the keywords like "Protestant" to find books you want.

The beginnings of  my understanding it was the Philippa Carr series (similar to the Morland Dynasty) that starts with "Miracle at St. Bruno's"

By What Authority by Benson

You can read it free online here: http://www.gutenberg.org/ebooks/19697

From my own collection ...

1. The Arm and the Darkness by Taylor Caldwell - many of Caldwell's books deal with religious topics; see also, Great Lion of God
2. The Gospel of Judas by Simon Mawer
3. An Instance of the Fingerpost by Iain Pears - fabulous read
4. Q by Luther Blissett - a bit dense
5. The Fire and the Light by Glen Craney - more about the Cathars
6. Wolf Hall by Hilary Mantel - didn't really like this one
7. The Illuminator by Brenda Rickman Vantrease

You are really talking about a shift that covers many many years and several sovereigns. Henry 8 made the official break, but his version of  'Anglicanism' was essentially Roman Catholic, just without the Pope having highest authority. He kept the structure and ritual intact.  His chamberlain was responsible for destroying the Catholic outposts in England---he raided the monasteries and convents of their riches and lands.  His daughter Elizabeth is usually credited with having stripped the Catholic liturgy down to its essence, which is pretty much the same today. Her Archibishop of Canterbury (essentially the old RC Bishop of London, and with Henry's break, the highest clergyman in the Anglican structure) is credited with authorship of The Book of Common Prayer---which represented a fundamental shift from Catholic doctrine. TBCP is the very first time that the liturgy was printed in book form so that the common man could follow along--in English, not Latin.  Groundbreaking. It also strips a lot of the ceremony from the liturgy and simplifies the language--and with one or two revisions over the years, is what the Anglican/Episcopalian religions use to worship today. Uprisings of underground Catholic nobles continued throughout Elizabeth's reign, as well as James', who followed her right up through the end of the 17th century--the Jacobean risings are a good example.

So there are actually a lot of HF titles that cover time periods within this century-long 'conversion'---it took a long time for the peerage and country-dwellers to really convert. Many rebellions were financed by Rome and Spain during the century--again, with a lot of HF written about it.  My best advice would be to study the history first--briefly--and then google novels about particular events in history that sound interesting.