Though its far from the only reason, one of the less discussed factors that plays into maintaining the Girl Show Ghetto is the perception created by Lifetime Movie of the Week, and Women Are Wiser. The expectation here is that a show featuring a female lead might be preachy and/or tend to bash men a lot, and this perception is not without merit.
Take the Big Three of DC Comics: Superman, Batman and Wonder Woman. Superman and Batman, whether their stories have depth or not, tend not to be allegorical or political (at least until Superman's 2011 reboot). But Wonder Woman has strong feminist themes. She comes from an island entirely populated by female rape victims where men are forbidden to set foot and stories focused on her outside her own title (and sometimes in it) will take pot shots at men (though Wonder Woman is shown to be above doing so herself, the writer will inject these themes into the narrative).
This creates a clear impression in the minds of potential male readers that if you pick up an issue of Wonder Woman, you can expect to be preached at. How many fans do you think are beating down the doors of their local comic book shop on shipping day for that opportunity?