Queen Elizabeth was only a moderate for the first half of her reign. In the second half, she was led by more radical ministers, who prompted her to persecute Catholics, due to the threat of Mary Queen of Scots. Priest holes were widely used in the Elizabethan period to hide Catholic priests. Elizabeth came in for criticism from both Protestants and Catholics, for neither taking a moderate route nor being truly protestant. 
Conflict over catholicism would continue after the reign of Elizabeth. James I and Charles I both stirred up controversy over catholicism during their rule. 
The reformation was painfully slow in England.
Elizabeth became more militant as her reign went on. Conflict over religion in England would remain in the Stuart period.