There is ample evidence to suggest that the Jews were a persecuted minority. You only have to look at the first scene containing Antonio and Shylock, where the 'merry bond' is made, to see that the Jews were treated badly and looked down upon. This becomes an important element when we consider Shylock's motivation for revenge later on in the play.
The jews were treated terribly in the merchant of venice because they had different beliefs to the catholics. An example of this is when Antonio spat on Shylock at the beginning of the play which was terrible as Antonio ends up using him to get money for Bassanio.
Hope this helps.