Terrorism, by definition, is the act of performing random acts of violence towards a civilian population for the express purpose of creating fear and uncertainty and is performed by persons with no definitive origin.
Al Qaeda wasn't targeting some person in the world trade center. They were simply murdering as many people as they could in the most arbitrary way to instill fear and panic amongst their enemies.
Moreover, if a military aircraft from country X wrongly bombs a building full of civilians in country Z then country Z has many options available to them.
Consider how much simpler things would be if the WTC had been attacked by say the government of Iran or some other nation state.
What's nice about nation states is that they are much easier to be held accountable.
The minute you give terrorists the same legitimacy as the governments of nation states you might as well throw up your hands and argue that criminals have their own legitimacy as well. Terrorists are just another form of violent criminal who have simply passed a threshold beyond what can be dealt with by civilian police forces effectively.