What is the conflict between Antonio and Shylock in The Merchant of Venice? Does it have any roots in religion?

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."