Wow, I was just complaining about that quote in another thread a few days ago...
I don't really want to get into a lot of the ideas of the movie as a whole (since it has just been too long since I have seen the movie), but I certainly agree that, in context, that line is not meant to be something the viewer should agree with.
Mostly, we are meant to believe that the line is flawed simply because it comes out of a psychotic villain's mouth, and the voice actor and animators put such a wonderful evil tone and wicked expression into the the second half of the line (the important half).
As far as I am concerned, I think that line exists solely to reveal Syndrome's ultimate motivation: he wants no one to be "super", meaning he wants superheros to cease to exist. The first half of the line ("if everyone is super") is a just a brief explanation of how (in his twisted mind) his current actions will lead to his end goal stated in the second half ("then no one will be"). Honestly, if you take the line by itself, even in context, it is pretty logically flawed... Of course, Syndrome is not one for logic, since his entire motivation for his rampant hatred of Mr. Incredible and evil deeds is the fact that Mr. Incredible didn't want a young brat tagging along on superhero work (which is a more reasonable stance than Batman ever took!).
Anyways, the movie itself challenges the very assumption behind the line (that all "supers" are equal). As I mentioned in another thread, look at the scene where Syndrome tries to pass himself off as a superhero/defender of justice in the final battle sequence of the film. Syndrome has all of the powers, all of the "super"-ness, thanks to his gadgets, but he fails to even stop a disaster of his own creation (that he rigged to stop when he told it to!). His obsession with power, massive ego, and disregard for society all mean that he will never be a superhero, even if he has powers (which is the very point of his big quote!).
Meanwhile, look at how Mr. Incredible changes across the course of the movie... He is truly heroic when he works behind the scenes to help an old woman with an insurance claim, but he only uses his powers to severely injure a defenseless (if petty) man. His powers and his heroic nature are seperate, not the same thing (like Syndrome implies in his line). In fact, the movie goes to pretty impressive lengths to show that Mr. Incredible is a far greater individual when he is acting like a normal father who happens to have super-powers, than when he is a superhero who happens to be a father. Some of my favorite scenes from the movie involve that distinction, really.
Besides, even ignoring all of that, you still have a guy trying to claim that just because everyone has superpowers, it would somehow make a man with super-strength, a stretchy woman, an invisible girl, and a speedster all "mundane". Even if that were all true within the context of that world somehow, it would not be applicable to D&D because that level of variation would still be incredibly interesting and diverse enough for anyone.
On a side note, I really think labels like "marxist", "fascist", "freudian", or whatever are terrible tools for trying to pick apart stories and ideas... I think it is something of a failing of academia (including my own college education, really), that it teaches people to interpret texts entirely through that kind of flawed lens.