It wasn't a cruise missile thats for sure. However, I think the U.S. government would have let the attack take place with prior intel. After all, the Secretary of State at the time came out and said that the use of planes as basically missiles was unheard of when in years past the U.S. air force and NORAD ran drills similar to those that occurred on 9/11. 100% interceptions successful.
On 9/11, three planes make it past the system.
I'm not saying this is what actually happened but its a possibility and a legitimate concern in my eyes.