To answer the question “Is the play a plea for religious tolerance?” in short, I would say ‘No’.
 
In no way can I find Shakespeare’s play The Merchant of Venice promoting religious harmony. Rather, modern critics call the play ‘Anti-Semitic‘, i.e., against the Jews. Shylock, the Jew received insults and injustice all his life. His desperation to get the bond was only his protest against the age-old insults and hatred the Jews received from the Christians. But the way the Christians showed their unchristian social attitude in denying him the justice puts them to shame.
 
Nowhere in the play the Christians characters like Antonio, Bassanio, Gratiano, Lorenzo and Portia showed the slightest weakness for Shylock. Rather, they did not miss any chance to insult him. On the other hand, Shylock wanted to befriend his Christian counterpart Antonio. But the Shakespearean audience, mostly Christians, have seen Antonio as a hero and Shylock a villain, just from their own prejudiced mind. 
 
This is not to say that Shylock did everything right and the Christians did everything wrong, but Shylock was more of a victim of religious persecution than a villain. In the play there is no message of religious harmony, but everything is against the Jews. It has been a play depicting class distinction and racial hatred.