Religious prisoners in the 16th century were seen as a special case. Many were kept in the Clink Gaol - a small lock up that became notorious for this purpose - or the Tower of London. Unlike ordinary prisoners, they were seen as traitors and rebels. They were treated worse than ordinary prisoners and were not allowed alms that would allow them to buy food in gaol. The first religious dissenters were seen in the Catholic Middle Ages but it was with Henry VIII's break with Rome and the death of the Catholic Martyrs such as St Thomas More and John Fisher that they came to the fore.
Twenty years later the role was reversed under Mary Tudor, a Catholic Queen, when Protestants were persecuted. Queen Elizabeth I wanted her subjects to be moderate Protestants (Anglicans) and both Catholics (seen as traitors) and 'extreme protestants' known as Congregationalists or Puritans were persecuted. However, Elizabeth refused to execute Catholics who did not accept Protestant beliefs and was only willing to execute those who tried to overthrow her.