Enotes has an excellent summary on how Jews were treated during the time Shakespeare wrote and performed Merchant of Venice. That information strongly suggests that he did not have much sympathy for Jews in general for he would have been very much in opposition to dominant ideology if he had. Yet, Shakespeare consistently sees into the heart of people, and he does give us various windows onto Shylock's resentment and hatred of Christians in the "hath a Jew eyes" speech and elsewhere. Some directors, emphasizing such passages and the ambiguity in others, perform this play in such a way that Shylock becomes a very sympathetic--although still malicious-- character. Link to the q & a section on enotes Merchant and then Jews.