A lot of the "truther" nonsense came from the day of the attack when nobody really had any idea what the hell was happening. It wasn't immediately clear that a plane hit the first tower to cause the damage, it wasn't clear it was an attack and not an accident until the second plane hit, and it wasn't clear the planes alone caused the collapse for days at least. Hell, for like an hour the Pentagon attack was considered either a potentially unrelated fire or a missile attack.
It's unfortunate that this at the moment reporting can reinforce conspiracy theories, but maintaining the uncertainty felt during the day provides a benefit. Much of the day was filled with shock and confusion, with everybody watching the news to try and figure out what was happening.