Harold Bloom, who himself is Jewish, writes that Shakespeare's
persuasiveness has its unfortunate aspects; the Merchant of Venice may have been more of an incitement to anti-Semitism than The Protocols of the Learned Elders of Zion, though less that the Gospel of John.
Shakespeare explores the culture of sixteenth century Venice which had its problems with unethical merchants who charged interest on loans and who conflicted with the Venetians. Shylock represents these unethical merchants--he says of Antonio, "I hate him because he is a Christian"(1.3)--who charged usurer's rates of interest on loans, who had no mercy upon those to whom they had loaned money. Portia's famous speech, "The quality of mercy," (4.1) expresses Shakespeare's Christian lesson.
The major theme of this play is mercy and forgiveness -- major Christian ethics. It is about how you should treat the people that you do not like. I think that this is conveyed through the way that Shylock wants to take the "pound of flesh" from Antonio as a way of getting revenge against him.
Not all of the play is about this (especially the part with Portia and her finding a husband) but the main theme is how you treat your enemies.
In a 1986 piece, Professor Bloom quoted a Professor J. Middleton Murry: "THE MERCHANT OF VENICE is not a problem play; it is a fairy story." He then suggested that the play is a problem play and not a fairy story. As implied here and elsewhere the play is both a problem play and a fairy story. In Cliffsnotes guide we find: When read in synopsis form, the story of [MV] seems extremely silly." One purpose of the fairy-tale element is to suggest that one not dismiss elementary matters and another may be that we should expect to find simple errors in the commentary, after all, the play is entertainment, among other things. One might then argue that the main theme of the play is that discourse is good. In ROMEO AND JULIET, Romeo, in his grief says: "O mischief, thou art swift / To enter in the thoughts of desperate men"(ROM5.1). The many links in MV to ROM suggest that the passage is of use when considering Shylock's behavior as it is thought that his wife has passed away.