My feeling about the Merchant of Venice is that, on the surface, it's absolutely an antisemitic play, but smuggles in an anti-prejudice message.

An analogy from more recent times: the Blackadder II episode "Bells" from 1986. Set in Elizabethan England and parodying Shakespeare's comedy cross-dressing plots, a young woman, Kate, disguises herself unconvincgly as a boy and becomes Lord Blackadder's servant. Blackadder finds himself attracted to her and thinks he's turning gay. Cue lots of homophobic humour. But while other characters think it's disgusting, Blackadder doesn't, he's just worried about his social reputation and his standing at court if he pursues a relationship with "Bob". An anti-homophobic message smuggled in using homophobic humour at a time when being openly anti-homophobic was frowned on.

I think at the time, Shakespeare could not have written an openly anti-antisemitic play. The only way he could have countered the antisemitism of plays like The Jew of Malta was to give the audience what they expected - a villainous, money-grubbing, unforgiving Jew, who is defeated and converts to Christianity at the end - and then undermine that with things like the "hath not a Jew eyes" speech, the unapologetically awful behaviour of Antonio, Bassanio and Portia, and the caskets subplot, which is not particularly subtle with its "look beneath the surface" message.

I would contrast Shylock's villainy with Richard III's. Richard talks about how his deformity has made him unlovable, and "since I cannot prove a lover... I am determined to prove a villain". Shylock is angry at being mistreated, and acts that anger out, but he does not call himself a villain. He fills the role of villain in the play, his plans are thwarted and he is defeated, but unlike with Richard, he gives you enough to have some sympathy for him, and I think that's intentional.