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.