The title of the play seems to refer specifically to Antonio, who is indeed the Venetian merchant of the story. This is odd, as Antonio is more of a secondary character, remaining offstage and silent through much of the story. Shylock, the Jewish moneylender, is far more central to the story. This raises the much-asked question of why Antonio is the title character and not Shylock or Portia, who also takes center stage in this play.
In fact, the play was first listed under a different title: "The Merchant of Venice, otherwise called the Jew of Venice." Perhaps the title was simplified when the play was later performed and published. It is possible that this was done to identify Antonio as the hero of the story. It has also been suggested that the title was clarified and shortened in order to avoid confusing it with Christopher Marlowe's play The Jew of Malta, which was published around the same time.