Throughout the novel Tom is the character most closely matching the concept of a villain.
Tom Buchanan is the villain of this novel and has Nazi-like theories of race.
We should qualify this statement, however, as Fitzgerald's novel is not a study of good versus evil like some other literary works, but instead depicts morality on a "grey scale".
None of the characters in the book are wholly "good" and none are wholly "evil". Gatsby, for instance, manages to retain a redeeming innocence to the very end, despite his morally questionable intention to lure Daisy away from her husband.
...his loyalty to his dream and idealism mark him as one of the tragic heroes in American literature.
Morally speaking, Gatsby cannot be fit into a single category. This is equally true of Daisy, Jordan and Nick.
Tom, however, has few redeeming qualities. His belligerent ignorance aside, Tom has no excuses for cheating on his wife, for beating Myrtle, or for adhering to doctrines of racial hatred.
These actions and traits characterize Tom as something of a villain, though he is not set in contrast to any representative hero. For this reason, we cannot accurately say that Tom is a villain representing evil. He is, simply, not a good person.