I'm sorry but it really seems like your just reading way too far into what superheroes and escapist power fantasy is supposed to be. Like Tippy above me said, nobody is reading superhero comics or Harry Potter and putting themselves in the place of random civilian #55, they are imagining being able to have superpowers themselves and going to Hogwarts to learn magic. Frankly that is the way it should be, nobody wants to read about the life of Joe Schmoe, faceless bureaucrat with the unenviable job of enforcing state child care laws and removing crying children and babies from their families, returning home every night to play video games and hang out with his friends; who then spends the occasional weekend biking in the mountains. I just described my own life, and I may be mostly satisfied with it, but I sure as hell don't want to read about it.
I want to read about people and places greater than myself, who do the things I can't or won't do. I want to travel to fantasy lands and extraordinary planets that no normal human could ever visit. That is what a good fantasy or superhero story does, it allows us an escape into things that can never be in reality. Yes, this sometimes means that there are unfortunate implications, but a good story will make them unimportant to the plot and keep our suspension of disbelief in tact. If you overthink the wizarding world in the Harry Potter books, then yeah the muggles get treated like crap and I will honestly agree that the muggle side of the story really gets no payoff by the end of the 7th book, but that's not really the point. We don't read Harry Potter to experience a moralizing tale about the Ubermensch, it's a somewhat simplistic fantasy story about good wizards fighting bad wizards, and a child growing up in that fantastic story. The average reader isn't thinking or identifying with the muggles in the story, he/she is imagining moving paintings, owls that deliver mail, magic duels at night, enchanted mirrors, and creatures right out of fantasy existing in the modern day, all set amongst an idyllic Scottish countryside. While the societal, cultural, and psychological effects of living in a society with a clearly superior class of people is an interesting setting for stories, that should hardly be the only focus in any story featuring super powers or magic.
As a final point, you may not like it, but it is something that I have experienced as true many times in my life, and that is that we are not all created equal in ability. To a child born with severe Fetal Alcohol Syndrome, a normal healthy person might as well be Superman to that child, because as much as they may try, they can never equal that average, physically or mentally. If I drop everything in my life right this second and spend every waking moment training for the Tour de France, I will never be able to win, simply because I am a severe asthmatic. Those people will always be faster, in a way they are the Flash to my normal human abilities. There is always someone faster, smarter, stronger, better looking, or more experienced than you, that is a fact of life; that does not mean that the best of the best should be able to discriminate or abuse those weaker, slower, or sicker than them, we must strive to create a society where even the weakest are at least given the chance to succeed and excel. Which is exactly what many superhero and fantasy stories do, superman does not lord his strength as the Ubermensch over the normal people, he is portrayed as all too human in his emotions, and feelings, he is shown with personal flaws and struggling to uphold noble ideals, and even sometimes failing. This is why DC and Marvel seem to have their setting stuck in a perpetual time freeze, with all the iconic heroes never aging but always being in the present day, so that they can focus on character and setting rather than trying to extrapolate out what the actual existence of superheroes would really do to society, I will give you that it's cliche and really kind of played out by this point, but taking the other road requires them to invent a very different earth that would bear almost no resemblance to where we live today.
To wrap this whole probably pedantic diatribe of mine up, feel free to hate on superheroes all you want, god knows there's plenty of bad stories and legitimate criticisms to lay against the tired old genre. Hell, I mentioned Superman but stuff like the end of the recent Man of Steel movie, that make you stop and say, "wait how many people probably died when that building collapsed?" are good points and when suspension of disbelief is broken we often start questioning everything else in the story as well.
But don't for a second sit there and try to extrapolate people enjoying the genre out into some commentary about how they are similar to supporting the silliness that is Social Darwinism, or the evil that is enforced eugenics. That goes past reading too far into something and right into the kinds of leaps of logic that started the theory of Social Darwinism to begin with.
