Three reasons why he probably wasn’t:
1) Sort of like ItcheSrulik said, it’s very likely that he was just pandering to the cultural biases of his time to make his works popular without having a confirmed belief in them. Which brings us to:
2) Like soliek said, the views in a work do not always (and very often b’davka don’t) reflect the true views of the author. Very often, they use such negative representations in order to satirize them. Case in point: Steinbeck. Many of his works have been deemed misogynistic. But if you actually read them to understand (or peruse any decent criticism on Steinbeck), you will figure out that the author actually represents women negatively because he is writing in the male perspective and is trying to show how flawed it is. It is very likely that that was what Shakespeare was trying to do with the Jews here. Which brings us to:
3)The Merchant of Venice was actually largely based on another play named The Jew of Malta, an anti-Machiavellian satire of Christian sovereignty cunningly cloaked in anti-Semitic trappings. So it is very likely that Shakespeare was extrapolating on that intent. Bear in mind that satirists of such highly sensitive subjects had to be very careful to disguise their intent so as not to about their own lynching.
Bottom line – before you jump to to unfounded conclusions, go read some literary criticism.