I think she means 'rotten' in a good way. From her epic Playboy interview:
PLAYBOY: Do you have a personal antipathy toward Jews themselves?
THOMAS: No. I think they're wonderful people. They had to have the most depth. They were leaders in civil rights. They've always had the heart for others but not for Arabs, for some reason. I'm not anti-Jewish; I'm anti-Zionist. I am anti Israel taking what doesn't belong to it. If you have a home and you're kicked out of that home, you don't come and kick someone else out. Anti-Semite? The Israelis are not even Semites! They're Europeans, and they've come from somewhere else. But even if they were Semites, they would still have no right to usurp other people's land. There are some Israelis with a conscience and a big heart, but unfortunately they are too few.
PLAYBOY: In the wake of your anti-Israel comments, a blogger from The Atlantic argued there's really no distinction between anti-Zionism and anti-Semitism. He wrote, "Thomas was fired for saying that the Jews of Israel should move to Europe, where their relatives had been slaughtered in the most devastating act of genocide in history. She believes that once the Jews are evacuated from their ancestral homeland, the world's only Jewish country should be replaced by what would be the world's 23rd Arab country. She believes that Palestinians deserve a country of their own but that the Jews are undeserving of a nation-state in their homeland, which has had a continuous Jewish presence for 3,000 years...."
THOMAS: [Interrupts] Did a Jew write this? [Editor's note: The writer is Jeffrey Goldberg.]
PLAYBOY: "...and has been the location of two previous Jewish states. This sounds like a very anti-Jewish position to me, not merely an anti-Zionist position."
THOMAS: This is a rotten piece. I mean it's absolutely biased and totally--who are these people? Why do they think they're so deserving? The slaughter of Jews stopped with World War II. I had two brothers and many relatives who fought in that war against Hitler. We believed in it. Every American family was in that fight. But they were liberated since then. And yet they carry on the victimization. American people do not know that the Israeli lobbyists have intimidated them into believing every Jew is a persecuted victim forever--while they are victimizing Palestinians.