You got me curious, so I googled "Ferengi" + "anti-semitism". I found a page devoted to the creation of the Ferengi characters, and it addressed the charge of anti-Semitism:

That's so astonishing to me, because Jews come in all shapes, sizes, forms; it was,just that the Nazis tried to impose a stereotype. I'd heard concern about that, but, you know something, there's been concern about every villain that's been invented.

Herb Wright, original creator of the Ferengi, in BEHIND-THE-SCENES: CREATING THE FERENGI

That's not the final word, of course. He talks about how he and Roddenberry consciously modeled them after the people they knew in the business. (But be careful you're not doing your own stereotyping by assuming that everybody in Hollywood is Jewish.)

When Gene asked me to come up with a kind of grand villain for the new Star Trek series, he said he didn't want to rely on the old stuff. Well, take a look at the Klingons; they were basically the Stormtroopers of space, and the Romulans were kind of like the SS of space. I went off to noodle what the look and shape and construction of this new villain would be physically and emotionally and to work out what their society would be like; basically I had to come up with a new world. That wasn't too hard. I just looked around at 80's America, where greed was good and Gekko was one of our heroes. I came back to Gene and I said, "Where are the carpet baggers? Where are the robber barons? Where are the guys where every time you turn around they're buying space ships out from underneath your feet or stealing from you?" He said, "Oh, yeah, yeah, that's a good idea." "Those guys," I said, "You know, like all the agents and lawyers we've ever been involved with." He laughed and said, "Love it." With the Ferengi, the idea is that profit is the most important thing. You always like to come out on top, and business rules supreme. Even when you die, the heaven you go to is in fact where they count up how much profit you have and give you a good table in front, while hell was the place that you'd go to penniless and have a damned future in which you would be taken advantage of every five seconds, which is the worst thing the Ferengi can possibly imagine."

Kind of ambiguous, isn't it?

I can only add that Quark's dialog on that DS9 episode the other night was chock full of contemporary Republican rhetoric: Grumbling about taxes, a minimum wage, taxes, pensions, taxes, anti-trust laws, taxes, and in general the destruction of time-honored Ferengi values. Looking for subtle clues suggesting anti-Semitism is one thing, but there was nothing subtle at all about Quark's parody of a Republican.

Like I said, it was an uncanny impression of Tom.