and soon that flight in Pennsylvania went down because (presumably) the passengers knew their plane would be used...

Actually that flight (#93) was taken down by an EMP burst fired from an F-16 scrambled from a squadron based in North Dakota. Government records show that all cell phone calls involving the passengers halted at 9:03 a.m., the same time that the transponder signal and cockpit radio went dead and presumably the same time the navigational electronics failed. The impact occured at 9:06 a.m., which is consistent with the scenario of a plane with dead engines hurtling out of control at that altitude.

Much cleaner than a missile strike, you see.