In most of the cases where the definite article is consistently used, it's because the name is more descriptive than anything else. For example, the Martian Manhunter is really more an epithet than a name. His name is J'onn J'onzz, and that's not a secret, but he is A) the last living Martian and B) the only Martian on Earth and certainly the only Martian detective on Earth. Thus, the definite article makes very good sense given that the epithet is really more along the lines of the way Batman is also called "The Caped Crusader".
Similarly, everyone pretty much knows who the Fantastic Four are, so Johnny Storm gets an epithet, "The Human Torch"; his sister, Sue Storm-Richards is "The Invisible Girl", and Ben Grimm is "The Thing"; while their leader gets the somewhat full-of-himself nickname "Mr Fantastic" -- but everyone knows he's Dr. Reed Richards.
By contrast, Bruce Wayne's identity is a secret, so "Batman" has become his alter ego's name, while many other epithets are applied to him (the aforementioned "The Caped Crusader", "The Dark Knight", etc). This same basic heuristic also makes sense for Superman, Daredevil, Iron Man (in the comics; in the movies, of course, Tony Stark is out of that particular closet), Wonder Woman, Spider-Man etc. Their superhero "names" have been applied to them by others -- often the press -- because their real names were secrets.
This is not a rule, though, but a heuristic, because, for example, "The Flash" is very rarely just called "Flash" except maybe in direct address, possibly because it just sounds funny. Similarly, "The Question" would just sound wrong as "Question", and lastly, it's almost always "The Hulk". Part of that, I suspect, is that their superhero identities are basically words for things being applied to people.
And then, sometimes, the heuristic is broken just because someone decides it would be more dramatic, or it fits their own aesthetics better. Batman is occasionally referred to as The Batman; Green Lantern and The Green Lantern are somewhat interchangable; the upcoming Wolverine movie is The Wolverine, etc.