An opinion survey carried out in Helmand and Kandahar provinces showed that 92% of the Afghan respondents (1000 men) had never heard of 9/11.
Most Americans are ambivalent about the Afghanistan War precisely because it is hard to dismiss the argument that the September 11 attacks were planned out there in some of 40 terrorist training camps that were aimed at waging war on the US.
If Afghans, 72% of whom are illiterate, have never even heard of September 11, then they have no idea why the United States and NATO are even in their country! And the entire lack of such knowledge would likely make them more hostile to that presence, since it would seem wholly unjustified and from out of left field to them.
Knowledge of the wider world is connected in part to information infrastructure. Afghanistan suffers from lack of electricity, which limits access to television and the internet. Internet penetration is only 3%, in part because of the high cost of satellite communications and the lack until recently of cheaper fiber optic cables. The satellite signals have allowed around 30% of Afghans to have cell phones.
But information is more available in urban areas such as Kabul and Mazar than in the mostly rural Pashtun south.
It is also possible that Pashtuns who had supported the Taliban are embarrassed by 9/11 and that their denials are a way of saving face.