The question posed her is one of a subjective nature. What this means is that you could potentially receive many very different answers based upon personal interpretations of both Antonio and Shylock. Depending on which character the reader relates to more, sympathizes with more, or even likes more, one could justify either character deserves sympathy.
This being said, I beleive that Antonio shold be sympathsized with more.
The reason for this is that, while both men were horrible to each other (both were prejudiced against each other), Shylock is the character who wants to publicly humiliate Antonio. Shylock is not satisfied with a repayment six times the amount of the debt owed. Instead, he wishes to claim the pound of flesh as promised upon inability to repay the initial debt.
This being said, while Shylock does stand to lose everything if a single drop of blood is spilled, he is the one who is influenced more by hatred than by the repayment of the debt owed. Shylock knew there would be a possibility that Antonio would not be able to repay his debt; therefore, Shylock enacted a penalty so inhumane one could only consider him monstrous.