Who was the real villain in "The Devil and Tom Walker"?

This is an interesting question, but I think the "correct" answer will strongly depend upon the reason the question is being asked. For example, if this is a comprehension question to see if someone has read the story, the answer may be a bit less nuanced than if it is being asked to question the role of morality and responsibility in the story.

Without getting too reductionist about the elements involved in the story, we...

This is an interesting question, but I think the "correct" answer will strongly depend upon the reason the question is being asked. For example, if this is a comprehension question to see if someone has read the story, the answer may be a bit less nuanced than if it is being asked to question the role of morality and responsibility in the story.

Without getting too reductionist about the elements involved in the story, we don't have too many factors to work with when we consider who we can blame as the villain. There's Scratch, Tom, Tom's wife, the people of Massachusetts, and possibly Captain Kidd. If we're considering things in terms of conflicts, such as man vs. nature, then we might consider religion, human nature, and society or social standards to be involved. 

Considering the way the question is phrased, I think we can eliminate Scratch as the real villain. Besides the question being a very leading one (suggesting that the "obvious" villain is not the real one), Scratch doesn't actually force Tom to do anything or commit any sort of crime, other than the murder of Tom's wife, but this is presented as hearsay anyway. We also can't really blame Tom's wife, nor the people of Massachusetts, since they don't do anything to significantly drive the story or provide a root cause of evil. 

Tom seems a likely candidate for the villain, but we could also argue that it isn't Tom himself, but the negative aspects of human nature which he embodies that are at fault; for example, his greed and miserliness, and his shortsighted pursuit of material wealth. So, the simple answer is that Tom is the real villain because he's the one who actually committed all of the evil acts in the story, but on a deeper level the villain is human nature itself.