I believe Shylock is the villian in the play very simply because he is the antagonist to Antonio. Since Antonio is the protagonist and Shylock wants to harm him, he is the villian. I'm sure arguments can be made that he did what he did because he was harshly mistreated, but regardless of this he is the villian. Shylock is probably not the only villian in the play, but he is for sure the primary villian.