Good question - both are plausible readings!
Shylock has taken the centre of most modern interpretations of the play (of the modern filmed version of the play which, with Al Pacino as Shylock, puts Pacino's face right under the title on the cover!) largely due to the extra frisson created post-Holocaust by the anti-semitism directed towards him. He is indeed a merchant, and his "bond" for a pound of Antonio's flesh forms the centre of the main plot of the play - though he does vanish from the last act altogether, forced to reform into a Christian.
Antonio, however, is also "bound", it seems, not just to Shylock, but to Bassanio, and - of course - his merchant ships are also hugely important to the play. He certainly, appears in more scenes and speaks more lines than Shylock. It is possible that Antonio, in Elizabethan times, was obviously a central character, and Shylock a grotesque, comic second.
There is something else to notice about the title though. It pulls out two of the key themes of the play: firstly the fact that almost everyone in the play could be a "merchant" - everyone is interested in accounts, deeds, worths, values, bonds, prices, gold (if you don't believe me, look for money-talking in Bassanio's election scene).
Secondly, that the merchant is "of Venice", a term which could ambiguously refer to a born Venetian or an outsider living there. Racism is always close to the surface in this play.