From what I remember hearing it wasn't that the planes themselves were faked, there were planes, but it is the plane itself that was faked, what I mean is that instead of it appearing to be a military plane on CNN like it was as you can see in some personal videos, it instead appeared to be a passenger plane.
Another thing is that if you watch Loose change 2nd edition final cut there is a part somewhere in the middle that explains how 1 or 2 of the planes later landed at an airport that had been evacuated, the passengers were taken off of the plane into an evacuated building near the landing strip and no one knows what happened to them after that. I have not looked into this anymore than what was on the loose change video.