Based on the text and historical context, it is clear that Shakespeare intended Shylock to be a villain. He does create some sympathy for the character, but it is widely later readings of the text from a modern perspective that paint Shylock as a victim. Here are a few examples of how Shylock is portrayed as the villain of the story.
He is a moneylender
The very fact the Shylock makes a living as a moneylender would be considered criminal in Shakespeare's day. Christians of this time viewed lending with interest as a sin. Members of the Jewish community were forced into this profession by necessity, but Shakespeare's audiences would likely have seen this as cruel and greedy behavior.
He demands a pound of flesh
If Antonio is unable to repay his debt he is obligated to provide Shylock with a pound of his own flesh. This would of course kill him. As demonstrated in Portia's final speech, this may be considered a demand devoid of mercy. Some consider this an exploration of the idealogical differences between the so-called Old and New Testaments of the Christian faith. From a mostly Christian Elizabethan perspective, this could be seen as an act of cruelty.
Jewish villains were common in the day
Many plays by Shakespeare's contemporaries portray Jewish characters as the villains. The mere appearance of a Jewish character in a play would often indicate villainy. It was a common archetype of the day. Modern readings, with less prejudice, have of course rejected this reading.