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.