Because 1. I don't feel that's what defines him as a person and 2. For his time (those being the key words) he was mostly progressive on that front and other fronts.
When it comes to Richard Wagner or Ezra Pound, both of whom said they hated the Jewish people and *actively* tried to hurt them (Wagner by writing pamphlets, posing Jews as the enemy of the Germany people and against them and trying to kick Jews out of music, including Mendelssohn, and Ezra Pound by hanging with and aiding KKK members, writing for Mussolini, likewise trying to expel Jews, and so on) then the personal flaws seep into their work and ethos, and then I give up on such people wholly.
For Shakespeare...
He did something no other playwright did at the time in at least making Shylock a complex character, giving him at least one speech to try and justify his actions (and you can--fairly--argue that he's arguing from a place of vengeance more than anything else, but I also think another line--"Forsufferance is the badge of all my tribe"--is telling in how Shakespeare at least considered WHY Shylock might be such a vindictive person to be important, and why he might have a valid point...you don't write "Suffering is my people's lot in life" for a group you totally and utterly despise) and giving a "good" Jewish character in his daughter Jessica.
And that's the key to it, really--
His "good" Jew is one who converts, happily, to Christianity for a loved one...and while today the idea of calling for Jews to convert is a nasty one, in 1594, saying that maybe, just maybe the Jews weren't intrinsically evil, treating them as actual three-dimensional characters and like REAL PEOPLE in his plays (rather than the all-evil "Jew of Malta" Marlowe created or the hordes of monster-like Jews Chaucer created) and making the claim "Oh, the Jews aren't evil, they're just wrong, they just need to convert to Christianity and then they'll be fine" was progressive.
The same way having a black man be the tragic (albeit murderous) hero and a white man be the evil villain (Othello) and having (often cross-dressing) women be the smarter halves of a couple and the heroines of a storyline was progressive...for his day. (I'd argue in some plays Shakespeare's still progressive with the way he portrays women, but I digress.)
Antisemitism isn't black-and-white, and I can both acknowledge Shakespeare was a product of his time while at least appreciating that (as far as we know) he didn't have the sort of wholesale hatred for the Jews that was common in his time...he took the time to give his Jewish characters decent motivations for what they do and say, good and bad, and even took the time to admit that the Jews were a long-suffering people, and for that, I'm grateful, and can enjoy him and his work.
(T.S. Eliot's trickier, as basically his problem with the Jews is similar--he's all about tradition and symbols and hates the "idea" of a Jew more than actual flesh-and-blood Jews themselves, he never made the kind of hate speeches aabout them Pound did--but he's hundreds of years later and so less acceptable. I still am able to say Eliot didn't go as far as Pound, didn't mind Jews in person--Pound refused to even be treated by doctors who had Jewish-sounding names--and probably never harmed anyone with his poetic Antisemitism, but while he's still my favorite poet of all time, it's still definitely the one black mark against him.)