While one could highlight the passages that function to humanize Shylock, as others have said, there's no way around the fact that Shylock is the vengeful villain, and the "triumph" of the play involves his forcible conversion to Christianity.

Some historical context helps make clear the ways in which Shylock's character is based off of and plays into anti-Semitic stereotypes. While the details of how Jews have historically been treated vary massively across time and region, a common trend in medieval Europe was for Jews to be banned from many occupations and pushed into occupations such as money-lending and tax collection, which were seen as "necessary evils." This move had several effects: first, it allowed Christians to distance themselves from these occupations, letting themselves feel economically pure while continuing to have these economic functions. Second, it allowed the ruling class to extract taxes from common people and position Jews to receive the angered responses to these taxes. Third, it set up the anti-Semitic association between Jews and wealth that positioned Jews as necessarily wealthy and money-obsessed.

While Jews were (at times) coerced into working as tax collectors and money-lenders, anti-Semitism framed them as being inherently vindictive, as being leeches on Christian and working-class society, and so on. Shylock as a character is a clear anti-Semitic caricature, pushing the idea of Jews as not only miserly debt collectors but also nearly inhuman in their desire for vengeance.

I would note that many of Shakespeare's plays do have a quality by which they can be interpreted through a variety of different lenses, and so they have often been transformed and retransformed by various generations.

That being said, if we're talking about Shakespeare's own personal intentions and how it would have been interpreted by audiences of his own time (back when these plays were written and performed), things become more difficult. It's hard to say what was in his mind and heart, but anti-semitism was deeply ingrained in Christian Europe, something which you should keep in mind.

On the other hand, Shakespeare's "hath not a Jews eyes" speech is a powerful piece of writing in the ways that it humanizes Shylock and his plight. Furthermore, consider that, throughout Merchant of Venice, there is a recurring theme concerning the ways by which people are judged unfairly by society, and by the people around them. We see this in the Prince of Morocco's plea for Portia not to judge him on the basis of his race, and we can see this in the example of Portia herself—perhaps the most intelligent and capable character within the play—whose options are limited on account of being a woman.

Yet, at the same time, it should be noted just how troubling Shylock is as a character. He is unquestionably the villain of the piece (he's a humanized villain, true, but a villain nonetheless), and one should be aware of the ways in which his characterization itself reflects anti-semitic stereotypes.

Finally, keep in mind the critical scene towards the end of the play, where Shylock is outmaneuvered by Portia (who is herself one of the play's protagonists) and is left utterly defeated by his opponent. With these factors in mind, I find myself doubting that advancing ideas of religious toleration would have been Shakespeare's original intent.

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.