is a reason behind the feud between them. Shylock says to Antonio:

"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."

In other words, Antonio has cursed Shylock for being a money lender, as "usances" refers to the practice of lending money and charging interest. Shylock believes he has handled this abuse with patience, as Jews suffer patiently and often at the hands of Christians who mock them. Antonio has abused Shylock and even spat on him because Shylock lends out money that belongs to him. However, Antonio now needs money from Shylock, which causes their conflict to become even more bitter.

Many critics, including the preeminent Shakespeare scholar Harold Bloom, have called the play anti-semitic. In his 1998 book Shakespeare and the Invention of the Human, Bloom charged that the play resulted in many centuries of anti-semitism in Europe, ending in the Holocaust. See the link to the Smithsonian article below for more information about the problematic nature of the play and the debate about whether it is anti-semitic in nature. There is no doubt that religion is at the core of the conflict between Antonio and Shylock. 

Yes, the conflict between Antonio and Shylock has some roots in religion.

The conflict between the two characters is not exclusively based on their religious differences, though. There is an economic conflict that exists between Antonio and Shylock as well. In Act I, Scene 3, Shylock tells audiences the three reasons why he hates Antonio.   

1. Antonio is a Christian and Shylock is a Jew. Shylock says, "I hate him for he is a Christian." There has always been some tension between Christians and Jews, and Shakespeare uses that conflict in this play.  
2. Shylock is in economic conflict with Antonio. Shylock is a money lender who charges high interest rates. Antonio, on the other hand, lends out money and doesn't charge any interest. This causes Shylock to complain, "He lends out money gratis and brings down/ The rate of usance here with us in Venice." Shylock is forced to lower his rates, which earns him smaller profits. Additionally, Shylock has a bad reputation because he is the money lender who charges high interest rates.  
3. Antonio publicly bullies Shylock. Of Antonio, Shylock says, "You call me misbeliever, cut-throat dog/ And spit upon my Jewish gaberdine."

Before the play even starts, Antonio and Shylock have a very antagonistic relationship. It drives the play’s most suspenseful plot elements. Antonio disapproves of Shylock’s financial practices and lends money free of interest, competing with Shylock’s moneylending. Shylock reports that Antonio publicly condemns his usury and hates him for being Jewish:

You call me misbeliever, cut-throat dog,
And spit upon my Jewish gaberdine...
And foot me as you spurn a stranger cur.

Antonio asks to borrow money from Shylock in order to lend it to Bassanio. Because Antonio is opposed to charging or paying interest, Shylock instead imposes a penalty if Antonio does not repay the sum within three months: he wants “an equal pound / Of your [Antonio’s] fair flesh, to be cut off and taken / In what part of your body pleaseth me.”

Shylock assures Bassanio he is joking, and Antonio is sure that he will be able to return the money on time. Unfortunately, both Antonio and Shylock have bad luck, and Shylock demands the pound of flesh. Shylock’s animosity towards Antonio makes it impossible to persuade him. Portia saves Antonio on a technicality, and the only one who suffers in the end is Shylock.

This relationship contributes much to the play. The bond enables Bassanio to woo Portia and then forces Portia to save Antonio for Bassanio’s sake. It creates tension as the audience worries for Antonio’s well-being and sympathizes with Shylock’s anger. It also drives a potential wedge between Bassanio and Portia so early in their romance.