Terra Firma is supposed to take place when it was aired--2003, no? A 9/11 reference doesn't seem out of place, especially considering what kind of man Jack Crichton is.
It only seemed out of place to me because, in my mind, Farscape took place in a slightly different universe from our own. Pop culture references? Sure, awesome! Those are fun. References to a tragedy that had JUST happened and that we were still hearing about almost hourly on the news? I just would have preferred it not mentioned.