Treating them like comedy bad guys was part of the problem. You cannot have a story line in which they claim that all cultures are equal and to not be judged... and then do so by treating the Ferengi (and Worf) as sources of disdain/humor.
This to me is a misunderstanding of TNG era Star Trek.
The federation in TNG era Star Trek don't believe that all cultures are equal and deserve not to be judged, they believe that it's wrong to interfere in the natural development of other cultures. One recurring plot line in TNG era Star Trek is a planet wanting to join the Federation and then it turns out they practice slavery or something. In these episodes, the antagonist will usually accuse the federation of judging them unfairly, and Picard will
go away and think deeply about the ramifications of judging other cultures not give a shit because slavery is wrong.
The standpoint of TNG is explicitly that the Federation is correct, and that opposing the federation is bad. The Ferengi, as a society and a culture, are bad. The Klingons, when they were first introduced, were bad. One common feature of Star Trek is that over time the portrayal of other societies softens and becomes more nuanced. It happened to the Klingons in TNG, it happened to the Cardassians and Ferengi in DS9. It even happened to the Borg (sort of) in Voyager. But Star Trek never comes from the standpoint that all societies are equal and that judging them is wrong.
Even as the portrayal of Klingons became softer, there are still elements of Klingon culture which are never depicted as admirable, and the position of the Klingons within the federation is consistently shown to be predicated on the fact that they've worked to reform the worst excesses of their society.
Personally, I don't like the prime directive. I feel that it's a fundamentally selfish philosophy which the show tries to present as altruistic and has to constantly find excuses to make it work despite the fact it obviously doesn't. But even as written, the prime directive never implies any kind of equal respect for all cultures, only not necessarily having the right to interfere.