No, the Ferengi were originally supposed to be one of the other "heavy" villains in the show since the Klingons were now our friends. They were never intended to be a joke but more of the humans having to look at themselves in the mirror and see their own past which is why the Ferengi are greedy predator capitalists. Not to mention stuff like Picard suggesting in EaF that the Ferengi "eat" their enemies and the Ferengi having played a role in the destruction of Picard's previous command.
It's just that their execution didn't play out right and they became jokes.