Masked superheros are, by their very definition, unidentified good-doing entities. In some ways, that's the magic of them. They're good people who do good for no reason beyond doing that good. And, for the majority of the heroes found in Watchmen, they seem to be abiding by that same expectation. At least, on the outside. In actuality, Sally Jupiter (Silk Spectre) used masked superheroes to grow in popularity. Bill Brady (Dollar Bill) was created by banks. Adrian Viedt (Ozymandias) created a line of merchandise. Edward Blake (the Comedian) ended up working for the government. They monopolized the publicity that comes from mysterious figures doing good. They are the ones who embodied the world of superheroes that Watchmen presented; a culture fascinated, almost obsessed, with them to the point that they became real. And these four used the obsession that, in our world, is just being used by movie studios to draw in audiences. No matter what world we're in, people like superheroes, and Watchmen is a world where those superheroes actually became real.
However, those four monopolizing media attention are actually alone among the Watchmen heroes. The others - notably, the masked ones - not only maintained their secret identities, but also were noted for actually doing the good that came with their names. Nite Owl II (Dan Dreiberg) and Nite Owl I (Hollis Mason) donned their costumes because of a genuine desire to do good. Rorschach (Walter Kovacs) decided to fight crime after the murder of Kitty Genovese. Hooded Justice, the first real-life masked hero, literally refused to identify himself, even after death. Mothman (Byron Lewis) wanted to fight oppression and corruption. Captain Metropolis (Nelson Gardner) wanted to eradicate organized crime. Their personal identities didn't matter; the only thing that did was stopping bad things from happening. They are, in essence, like the superheroes featured in our comic books; people who maintain their secret identities to their own detriment. They are the heroes Watchmen readers would expect to find in a comic book - the traditional masked do-gooder.
One of the further themes that's scattered throughout Watchmen, among the disparity between media presence and secret identities, is the discussion of homosexuality among the groups of heroes. Out of the thirteen members of both the Minutemen and the Crimebusters, three were gay/lesbian: Captain Metropolis, Hooded Justice, and Silhouette - Ursula Zandt. While this isn't shocking on its own, it is when one considers the fact that superheroes (more commonly, mutants of the X-Men universe) are almost universally accepted as representations of the LGBTQA+ community. They embody the concept of a group shunned by normal society because of something strange or something that needs to be 'fixed'. Watchmen, however, doesn't touch on this comparison. The relationship between two characters (Captain Metropolis and Hooded Justice) is a well kept secret and the outing of the third (Silhouette) leads to her being excluded from the group of heroes.
A possible reason that Watchmen is able to avoid that comparison is the fact that the majority of the costumed heroes it portrays are bored wealthy people who have enough time on their hands to go gallivanting around a city in a costume, not troubled men and women who are driven to do good despite their terrible situation. Thus, the very concept of the Watchmen hero is different than that found in other stories of the genre. The isolation of the heroes is spawned from their wealth and brains rather than from some physical or social distinction that makes them different from everyone else. Some of the heroes - Rorschach, Silhouette, the Comedian - do follow the now traditional super hero path of rising above a traumatic event, but, just like the homosexual members of the crime fighting gangs, they're in the minority. They're not the story Watchmen seeks to tell. Sure, they, along with the wealthy heroes, all showcase the loneliness that comes from being different. But it's a different sort of loneliness. A different kind of isolation.
The isolation of Watchmen heroes is not because they're different for any discernible reason. In fact, it's barely there at all. They still engage in normal society, they still interact with each other. Their isolation is self-imposed rather than inflicted upon them by society. This is where they, at their core, differ from the rest of their genre. They do not exclude themselves physically - save for Dr. Manhatten (Jon Osterman), though he is the only one among them with actual powers - and, really, they don't do it socially either. The only time they do is when they make the final decision to keep what Adrian's done a secret. And the reason they decide they're able to? They're superheroes. By having made that choice years before, the Watchmen heroes mentally set themselves above the rest of the world. They decided that they had the authority to make choices over life and death, despite what the government had to say about the matter. After all, the only people left at the end were those who because heroes to be heroes, not for any publicity or other motives. They're the ones who do it because they believe they need to, and they're the ones who are most isolated out of them all.