Today we know the play as simply The Merchant of Venice, which seems to refer to Antonio, who is just that: a merchant living in Venice (as opposed to, say, Shylock, who is a moneylender living in Venice).
Sounds simple enough, right? Wrong. So wrong.
Keep in mind that play titles were a little more elaborate in Shakespeare's day than they are now. In 1598, when the play was first listed in the Stationers' Register (a big record book where all plays were entered for publication), the entry read: "a book of the Merchant of Venice, otherwise called the Jew of Venice."
For some, the Station's Register entry raises a question about who the play's "hero" is—Antonio (the merchant) or Shylock (the Jewish moneylender). This ambiguity about whose side we're supposed to be on spills over into the action of the play, where Shakespeare portrays anti-Semitism but also offers a sympathetic portrait of Shylock. Still, others think the alternate title (Jew of Venice) clearly makes Shylock out to be the bad guy because the title sounds a lot like The Jew of Malta (c. 1589), a popular and blatantly anti-Semitic play by Christopher Marlowe.
To complicate matters, the title page for the first Quarto edition of the play (printed in 1600) is completely different. Here's what it says:
The most excellent
Historie of the Merchant
With the extreame crueltie of Shylocke the Jewe
towards the sayd Merchant, in cutting a just pound
of his flesh; and the obtaining of Portia
by the choice of 3
As it hath been divers times acted by the Lord
Chamberlaine his servants.
Written by William Shakespeare.
The title page of the first Quarto pretty clearly suggests that Shylock is the villain. You can check out a facsimile of the original here.