I think the best example of prejudice in Shakespeare's "The Merchant of Venice" is the prejudice that exists between Christians and Jews. Antonio is a Christian and Shylock is a Jew. The two men cannot stand each other, and it is not because they have different ideas about how business should be done. They do not like each other because of their individual religions.
"How like a fawning publican he looks!
I hate him for he is a Christian..."
The play also contains racial prejudices as well. Portia is an in demand, wealthy, attractive woman, so much so that her father has potential suitors take a test. Portia herself is very discriminatory toward some of these men. For example:
"If he have the condition of a saint and the complexion of a devil, I had rather
he should shrive me than wive me. "
In other words, Portia is saying that it doesn't matter how good and nice and honorable the Prince of Morocco is. She will not consider him as a potential husband because he is black. She equates dark skin with the devil.