What points prove that Antonio is the villain in The Merchant of Venice?

Primarily, it is Antonio's treatment of Shylock which provides support for this contention. One can also assert that Antonio is but a symbol of the inherent faults existent in the society he represents. Be that as it may, Antonio displays a number of unacceptably vile characteristics, as Shylock so pertinently points out:

He hates our sacred nation, and he rails,
Even there where merchants most do congregate,
On me, my bargains and my well-won thrift,
Which he calls interest.

There is no real justification for Antonio's hatred of Jews except that they are of a different faith. Furthermore, it is apparent that Antonio makes a point of publicly denouncing Shylock because he lends out money at interest. These actions indicate a profound and unjustifiable prejudice. One would expect better from one who deems himself Christian, for it preaches forgiveness and tolerance, qualities that Antonio does not display towards Shylock at all.

When Shylock later meets Antonio and talks about the loan, Shylock further emphasizes the abuse that Antonio seems eager to dish out:

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 ...

... Shall I bend low and in a bondman's key,
With bated breath and whispering humbleness, Say this;
'Fair sir, you spit on me on Wednesday last;
You spurn'd me such a day; another time
You call'd me dog; and for these courtesies
I'll lend you thus much moneys'?

Antonio's actions make it obvious that he despises Shylock. It is ironic that he now approaches the one he deems his enemy, for financial help. This somehow smacks of hypocrisy, for if Antonio is so much against usury, which he deems a pernicious sin, why would he consciously and willfully support one who practices it? He could have asked one of his wealthy Christian friends to extend Bassanio the loan with him as guarantor. He surely must have realized, beforehand, that Shylock would charge him interest? The fact that Shylock is prepared to dismiss the interest later, cannot be used as an excuse.

Furthermore, after Shylock has been found guilty of attempting to bring harm to a citizen of Venice, it is Antonio who beseeches the court to mete out probably the harshest punishment Shylock could ever face. He asks the court to demand that Shylock, who is a deeply devout Jew, change his religion and become a Christian. 

Antonio's request represents his bitterness and resentment towards Shylock and it is obvious that he wishes to hurt and humiliate him in the harshest possible manner. His request is spiteful and vindictive. In fact, he agreed to the terms of Shylock's loan, knowing full well that Shylock probably had an ulterior motive. He signed the agreement against Bassanio's advice and his better judgment.

Although Shylock himself is presented as materialistic, resentful, bitter and vengeful, one can only assume that the last three qualities of his skewed nature were in retaliation and defense to Antonio's intense loathing.