Surely, though, they're ALL Products Of Their Times - "a true, prove able [sic], dyed in the wool villain" is a hard creature to find. As the programme on Richard III showed so well, there will be people ready to vilify someone others will passionately defend.
"Bloody" Mary Tudor: her heretic-burning was on a miniature scale compared to antics on the Continent; persecution of Catholics under later monarchs was far more widespread & systemic than Mary's (admittedly v dramatic & unpleasant!) antics; she was motivated by feeling she had a duty to ensure England remained a Catholic country after her death; she was operating within a society where brutal physical punishment was the norm.
Thomas Howard was hardly alone in ruthless ambition. Made more famous by Philippa Gregory's books, maybe?
Cromwell I do consider to be A Villain but lots of that's because to my grandmother "Cromwell" was the c-word 
There is a possibility his religious fanaticism was the result of a nervous breakdown, which casts a different light on things. Absolute crushing of dissent was broadly agreed to be the only was to gain & maintain political & social stability. Brutality & violence was completely normal at this point in time. With regard to the Irish campaigns it is worth noting that the Irish were considered by many to be sub-human - popular contemporary understanding would have been more pest-control than massacring other humans. He remains very popular in some circles, having been lauded by C19 historians as A Great Man etc.
Matthew Hopkins - again, very small beer compared to continental efforts. Surely the greater villainy is the context in which he was operating? People believed in - & were terrified of - witches. Plenty of people were tried & convicted without his involvement. His actual power wasn't all that impressive: were the people who listened to him & magistrates who tried & sentenced "witches" not in fact the more villainous?
Henry VIII did still have a need to secure his power, albeit not such a struggle as previous monarchs had had - hence his fixation on the subject of the succession. You can see his Reformation as part of the broader context of religious change. While gluttony, lechery & avarice are a long way from desirable character traits, do they really make him a villain? More a deeply flawed human being, surely?
Elizabeth was incredibly self-absorbed & rather power-crazed. Also had a touch of Wonderland's Queen of Hearts about her, no? She had a need to demonstrate authority (of a peculiar gender-constrained type) & had to face things like the Armada.
Agree with Magrathea's assessment of Richard I & John. Have a certain sympathy for James the 6th & 1st though: it's fairly clear/sure he couldn't help dribbling. It's thought he had incredibly bad hayfever. His obsession with the paranormal did lead to a lot of awfulness, but again, that sat well within the broader context of the time. The King James Bible was a massive achievement, too.
So yes. We are all products of time & circumstance & context & chance, historical figures no less so. Up until recently brutality; discrimination against/vilification of certain groups; fixation on a certain world order in the interests of Pleasing God; & in general a very harsh world was completely normal. Unlikely to produce lovely fluffy leaders/figures of prominence...