This is a very good question because we generally expect protagonists to be good and noble and trustworthy examples of how to live in similar situations. However, Heathcliff, though he at first rises above his obstacles, becomes torn with bitterness, hatred and desires for revenge. These traits do not ring true with the ideal of an heroic protagonist.
Nevertheless, when you realize that the conflict of Wuthering Heights is the conflict of "man against himself," the situation of Heathcliff as protagonist becomes a little more clear. (This conflict applies to Catherine, the second protagonist, as well as to Heathcliff.) Heathcliff's struggle is against his own dark nature and choices. In other kinds of conflict scenarios, the conflict comes from external elements or individuals. In Wuthering Heights, the things that Heathcliff (and Catherine) has to battle against and overcome arises from within himself. This creates a blurry edge to the ideal definition of protagonist.
When you consider Heathcliff's character traits at the beginning of the novel and then consider his later rejection of destructive traits and subsequent regnewal of admirable traits at the conclusion of the novel, you can see more clearly how the wickedness in the body of the story stems from the protagonist's inner conflict instead of stemming from an antagonist's attempts to overpower a protagonist.
In summary, Heathcliff is the protagonist with noble character traits (seen early in the story) who battles the conflict from the antagonistic hatred within himself. Like all good protagonists, Heathcliff does overcome and win the conflict in the end. This does then give us a model and an example to follow should it so happen that we ever erroneously and grievously give in to our capacity for hatred and revenge.
