It sure does feel as if William Shakespeare is prejudiced against Jews in The Merchant of Venice, and there was a strong anti-Jewish sentiment in Shakespeare's England; however, a careful reading reveals that his presentation of Shylock is more due to his being a villain than his being a Jew.
This play is about two opposing world views. One represents the best of Christianity, the quality of mercy, unmerited and undeserved. That view is best expressed in perhaps the most famous lines in the play:
The quality of mercy is not strain'd,
It droppeth as the gentle rain from heaven
Upon the place beneath. It is twice blest;
It blesseth him that gives and him that takes.
`Tis mightiest in the mightiest, it becomes
The throned monarch better than his own crown.
His sceptre shows the force of temporal power,
The attribute to awe and majesty,
Wherein doth sit the dread and fear of kings;
But mercy is above the sceptered sway,
It is enthroned in the hearts of kings,
It is an attribute of God himself
And earthly power doth then show likest God's
When mercy seasons justice.
This presentation of mercy is the best of Christian principles. It is the highest form of love for one's fellow man and comes directly from the heart of God. Mercy is the best way man can demonstrate God's love to others, and it is a blessing both to the recipient and the giver of mercy.
In contrast, Shylock represents a world view that suggests the only important thing is money and more money. Shylock certainly becomes a dramatic foil to this idea of mercy as he is bent on exacting his pound of flesh from Antonio. Shylock is the antithesis of merciful; his "black-heartedness" makes the "whiteness" of mercy shine brighter.
We know that Shakespeare's Portia, a Christian, is not deterred by the skin color or religion of the dark-skinned Moroccan prince who plays the game of chance to win her hand. This indicates that Shakespeare makes his judgments about people based more on their characters than on their race or religion. In fact, Antonio is the supposed "good guy" in this play, and he is nothing short of cruel to Shylock. He refers to him as a dog and worse. Shylock rightly points out that even though Antonio (along with Bassanio, Gratiano, Salerio and Solano) calls him a dog and a beast, he is certainly willing to come to Shylock when he needs money.
Signior Antonio, many a time and oft
In the Rialto you have rated me
About my moneys and my usances:
Still have I borne it with a patient shrug,
For sufferance is the badge of all our tribe.
You call me misbeliever, cut-throat dog,
And spit upon my Jewish gaberdine,
And all for use of that which is mine own.
Well then, it now appears you need my help:
Go to, then; you come to me, and you say
'Shylock, we would have moneys:' you say so;
You, that did void your rheum upon my beard
And foot me as you spurn a stranger cur
Over your threshold: moneys is your suit
What should I say to you? Should I not say
'Hath a dog money? is it possible
A cur can lend three thousand ducats?'
In this case, Shylock is the one in the right and perhaps acts more like a true Christian by loaning the money.
In short, while Shakespeare clearly depicts the villainous Shylock as a mercenary and vengeful Jew, he does not endorse the treatment he receives at the hands of Christians such as Antonio. Shakespeare does use the Jewish moneylender stereotype to shape Shylock, but Shylock certainly could have been something other than a Jew.