It is said approximately the same amount of Catholics died when Elizabeth was queen, but the difference is that they took place over her forty four year reign, obviously there were people of note such as Mary Queen of Scots, Anthony Babbington and Robert Devereux.
Mary punished those who were not of the same religion as herself, where as Elizabeth executed those who plotted against her. Many Catholic held important positions throughout Elizabeth's kingdom and if these people were loyal to her and discreet, they were left alone.
The number of executions carried out by Henry VIII range from 57,000 to the 72,000 (so says Raphael Holinshed’s Chronicles) this takes into account the mass murder following the Catholic rising known as the Pilgrimage of Grace. In Henry's son Edward VI reign there was the massacre of more than 5,500 Cornish Catholics after the Prayer Book Rebellion.