Stereotypes are ugly, Shmoopers. And persistent.
The stereotype that Jewish people have big noses was even old 500 years ago, and Marlowe wasn't about to let it go without milking it. When The Jew of Malta wasoriginally staged, the man playing Barabas wore a large prosthetic nose. But does the nose do anything besides identify Barabas as a Jew?
Take the moment that Barabas tells Ithamore to be a heartless criminal who hates Christians. Ithamore's response is "Oh, brave, master, I worship your nose for this!" (2.3.174). In other words, Ithamore's reply isn't, "Gee, you're so evil, I love it!"; it's "Dude, you are so Jewish. Let's go get those Christians."
What's more, Barabas's demand that Ithamore be void of "compassion, love, vain hope, and heartless fear" (2.3.171) is attributed to Barabas's nose, and therefore his Judaism. And then Ithamore tells Abigail "I have the bravest, gravest, secret, subtle, bottle-nosed knave to my master that ever gentleman had" (3.3.9-10). Notice how the emblem of Barabas's Judaism—his 'bottle-nose'—gets mixed up with his secrecy and knavishness?
Finally, when Ithamore tells Barabas that Friars Bernadine and Jacomo are approaching, Barabas replies that he "smelt 'em ere they came" (4.1.20), as if he's a kind of Jewish bloodhound that can scent out Christians. Sure, Ithamore's remarks are partially intended to be comic. "I worship your nose"? Yeah, we laughed.
But it's not really a laughing matter. All of Barabas's worst qualities seem to come down to that big honker—and to his religion.