This is a really good question, one which still has literary critics puzzled after four centuries. The identity of the antagonist of William Shakespeare's play The Merchant of Venice is open to some interpretation, as is the identity of the merchant mentioned in the title. 

The 1600 printed edition of the play (I have linked the title page, below) makes it clear that Shylock is the villain and Antonio is the merchant, but that is not the title registered in the Stationer's Register (the place where all plays were registered in order to be published) in 1598. That entry (linked below) lists the title as "The Merchant of Venice, or otherwise known as the Jew of Venice." The title probably does refer to Antonio, but this is an interesting discrepancy which makes one wonder if Antonio really was intended to be the merchant of Venice.

That being said, it is likely that Antonio is, indeed, the merchant to whom the title refers, and the reason you and others have asked the question, I think, is because Antonio is not a particularly admirable character. If the play is named after him, we rather expect that he is a person we either want to emulate or learn from, and that is not particularly the case with Antonio. 

Antonio is seen by some as a Christ figure, compassionate and giving to his friend Bassanio, even to the point of sacrificing his life, which is what would have happened if Shylock had exacted his pound of flesh. While that is one aspect of his character, there is certainly another side, which he displays in all its ugly glory toward Shylock.  When Antonio needs Shylock to loan Bassanio money, Shylock reminds him of how Antonio has treated him:

Signior Antonio, many a time and oft
In the Rialto you have rated me
About my moneys and my usances:
Still have I borne it with a patient shrug,
For sufferance is the badge of all our tribe.
You call me misbeliever, cut-throat dog,
And spit upon my Jewish gaberdine,
And all for use of that which is mine own.

Antonio not only does not deny the charges but adds,

I am as like to call thee so again,
To spit on thee again, to spurn thee too.

Even worse, at the trial Antonio (through Portia, his lawyer) practically begs Shylock to show him mercy; Antonio gets it through the judge, but he does receive mercy. When Shylock asks for the same from Antonio, no mercy is given.

It is difficult to believe, then, that Shakespeare names the play for Antonio because he is such a stellar character after whom we should model our lives. So we are left with the rather mundane conclusion that the play is named after Antonio, a merchant, because he is the common thread between all the major characters in the play. He is connected to Portia through Bassanio, to Shylock, and virtually every other character in the play. In effect, then, it is Antonio the merchant's story, so it is called The Merchant of Venice.

The play could be named after any of the major characters or a theme of the play. It did not have to be named after Antonio, who happens to be the merchant of venice. It could have been named after Shylock, and called The Money-lender of Vencie, or after Portia, and called The Advocate, or after one of the themes, and called The Caskets, or The Choice, or any other choice of names, of which there could have been many many.

The choice of Antonio, the merchant, as the name of the play, focusses our attention on all the Merchant themes, or as they are called, the mercantile themes.

What are the themes of the mercantile life? What experiences do merchants encounter, and remember, these are people who start business ventures, or sink a lot of their money into a business venture that someone else is starting.

It is the life of the mercantile adventurers. What kind of life do they follow? What kind of risks do they take?

A merchant can strike it rich and become a millionare, or their project could fail and they would be left broke.

It is the range and the dynamism of mercantile experiences that captures Shakespeare's imagination. We are all merchants at some point in time. We all gamble everything, and take risks with everything, whenever we make really important life decisions.

Shakespeare explores the nature of decision making and risk taking.

This is why he chose the merchant, Antonio, as his title character.

-Robert Einarsson operates Knucklehead Books, a publisher of upper-level Language Arts material from the neo-Scholastic or Middle Ages world view.