I would have to agree that he was definitely more of a hero than a villain. His role in bringing about Parliamentary rule was critical. His role as a military leader can not be overlooked either.
I will have to go with hero if those are my two choices. The reason that I come down on that side of the question is that I think that the move towards Parliamentary government was one of the most important moves in British history (and maybe in the history of the world).
I know that Cromwell was not without his flaws. However, what he did was really important. His actions were so very important in reducing the power of the British monarch and in increasing the power of Parliament. This, in my opinion, did a great deal to help Britain become the freest country in the world at Cromwell's time.
So, to me, Cromwell is like Thomas Jefferson or someone like that -- he has obvious flaws (Jefferson had slaves, Cromwell became Lord Protector), but his contributions to a really important trend in history make him a hero overall.