9/11 is not the only terrorist act to have impacted literature or cinema. Iain Banks wrote a story about the Lockerbie Disaster, for example (I forget the title, and it's not sf anyway). Most sf written about terrorism, I suspect, will have been of the flag-waving kill-the-nasty-terrorists variety. Popular entertainment tends to reflect social concerns, after all.
Of more recent vintage, there
Battlestar: Galactica, of course. And, while it's an indirect connection, there's also
Glorifying Terrorism (see
http://rackstrawpress.nfshost.com/).