In truth, Mary had many reasons to dislike Cranmer, though I obviously don't think Cranmer's intentions were ever to hurt or anger Mary. He was simply doing what his king wanted, and he did his job so well that he was regarded quite highly by members of the court. Another thing that separates him from Mary in those days, was his deep sympathy and affection for Anne Boleyn, whom Mary absolutely despised. While Mary saw Anne as the reason for her mother's banishment and death, as well as her own unhappiness, Cranmer saw her as the key figure in turning England from the Catholic faith and recognizing the "new" religion - which would become the Church of England. He and Anne were allies, while Mary and Anne were enemies.
The religious divide between Cranmer and Mary is really what sealed his fate. While he served King Henry, and later King Edward VI, he remained an invaluable Archbishop of Canterbury - because those two kings were (or became, in Henry's case) openly protestant (or Anglican). Mary, on the other hand, was devoutly Catholic, as we all know. Her beliefs in her faith were so strong that she thought anyone who was not Catholic was a heretic and deserved death. I would think that, when Edward VI died, Cranmer must have felt a bit uneasy knowing that Mary I would take the crown (of course, after the whole Lady Jane Grey mess).
This is where it gets truly interesting! Cranmer was given one final opportunity to recant - this time in public during a religious service. He wrote a speech that was published after his death, and began speaking at the pulpit about his submission to Queen Mary and the Catholic faith. However, he ended the speech completely unexpectedly, ignoring what he had written. He officially renounced the recantations and said that he would punish his hand for writing those untrue statements by burning it first at his execution. He referred to the Pope as "the anti-Christ" and publicly refused him. He was then pulled down from the pulpit and dragged to the stake - keeping true to his word as he placed his right hand into the flames as they swirled around him. When his right hand had burnt completely and the flames were rising up around his body, he reportedly looked up at the sky and yelled "Lord Jesus, receive my spirit...I see the heavens open and Jesus standing at the right hand of God!"
So, it's a bit difficult to sort out my feelings about this event. On one hand, I can understand why Mary had such an intense hatred towards the man who, as she saw it, ruined her family and her life. She saw him as one of her sworn enemies, and must have relished the opportunity to bring him down when she was Queen. However, I obviously feel extreme sympathy and sadness for Thomas Cranmer, who served his kings well and ultimately followed his heart in religious matters. Although he recanted in order to try to save his life, he ultimately died a true martyr for the protestant reformation, leaving no one to wonder what his true opinions about religion were. So, in conclusion, I must take Cranmer's side on this. From what I've read about him, he seemed like a truly good person, who certainly did not deserve the cruel fate he received.
Rest in peace, Thomas Cranmer!!!