I was recently working my way through Jonathan Hickman's run on Fantastic Four and it struck me how explicit the reference to the destruction of New York was made during the proceeding alien invasion storyline. Sue Storm (the super-mom of the group) demands that her fellow heroes move the battle with the invading Kree from the city's skyline to the ocean (why the ruler of the oceans, Prince Namor, has no problem with this is, I guess, because he's all googly eyed over Sue). And after the battle, the superheroes are shown helping rebuild the damaged city. This kind of real world destruction was so unimportant to superhero comics in the past that it became a central joke for a miniseries made back in the 80s called Damage Control about who actually does all the cleaning up. That's what the terrorists did to us, made it impossible to imagine a fantasy where real people aren't being hurt by collateral fallout from cataclysmic battles between superpowered beings.
Contrariwise, Slavoj Zizek has suggested 9/11 was a soporific, that it placed us in slumberland where American fantasies could take hold once again ("virtualization," he called it). The terrorists gave us real nefarious villains to which we could be safely opposed. The prominent media reaction, as he took it, like that of the typical superhero narrative, dehistoricized the attacks, setting them in the perpetual present of an endless comic book (or Hollywoodian virtual) world, where the action becomes one of pure villainy for villainy's sake, motivated by nothing but pure evil ("they hate our freedom," etc.). As Dan Hassler-Forest puts it in his book, Capitalist Superheroes: