That is to say, does Mary get a bad rep because the country never went back to being Catholic and the winners write history? Or was she really a lot worse with respect to persecuting the other side?
On one hand, Mary was actually a lenient, merciful person. She was ready to pardon Lady Jane Grey, until the Wyatt Rebellion forced her to change her mind: something that her far-bloodier father Henry VIII would not have hesitated over for a moment. Though she was certainly devout, her tally of 280 or so burnt heretics perhaps was not that great by 16th c. standards. But, on the other hand, it was substantial, considering it was done over only three years, from 1555 to her death in 1558. And it differed from previous English persecutions: they didn't kill as many people. When Archbishop William Warham went after 46 Lollards in 1511, for example, only 5 were burnt. It was typically the leaders who got the bonfire . Like Thomas Man, a wandering preacher who was burned in Smithfield in 1518. Mary went after even the lowliest, like the Colchester Martyrs, and went for them root and branch, not only burning modest tradesmen but their wives as well. That made her an easy target in John Foxe's Book of Martyrs.
She was also an unsuccessful monarch, lasting only five years, leaving no heir, and losing Calais, so it was easy to cast her as a villain. And, in the tradition of winners writing the histories, of course the end of Mary I and Catholic rule was seen as a victory for the Anglican Church. Eamon Duffy challenged that in his book, The Stripping of the Altars, ( and expanded it in his later Fires of Faith ) reasonably asking the question, why was it such a bad thing for England to have become Catholic again? And wouldn't it have been just fine, staying that way?
Comparing her to Elizabeth, however, is difficult. Elizabeth had a much larger political problem with the Catholic church than Mary had with her heretics: the Pope did not regard her as legitimate ( because Henry could not legally have divorced Catherine of Aragon) and said so: so she was under real threat. Her cousin Mary ( of Scots) was far preferable to Catholics and the center of plots, which is why Mary eventually had to be executed. It is quite hard to separate politics, economics and religion at this time: Mary I saw heresy as a terrible danger to her subjects' salvation. Spain's Philip II saw his elimination of heresy to be practical foreign policy, a mission handed to him by his father Charles V. But Elizabeth could be simply worried about the simple loyalty of her Catholic subjects, regardless of doctrine. The Jesuits coming into the country were trying to unseat her, and asking for assistance from the Catholic English, which they sometimes got: there was , for example, the Ridolfi Plot involving the Ear of Arundel and family. Elizabeth did not, however, go after the Catholics root and branch- plenty managed to keep a low-enough profile to survive. And she also had a very, very, long reign compared to Mary's, so you can't really just compare numbers: if she had kept Mary's pace, after 45 years she would have burned 2,240 people.