A little historical perspective here.

The dominant people in what is now Afghanistan are the Pashtuns. However, less than half the Afghans are Pashtuns, and half of the Pashtuns live outside Afghanistan. During the early 18th century, the Pashtun dynasty in Kabul ruled Afghanistan plus much of what is now northern Pakistan, all the way down into the Punjab. First the Sikh state and later the British nibbled away at Pashtun inhabited land on the Indus side of the mountains. The modern border (the Durand Line) was drawn in 1895, after the Second Afghan War, and it marks how far the British thought it prudent and profitable, in the light of Afghan resistance, to push their authority. The resulting Afghanistan was an ethnic hodgepodge, ruled from Kabul, that served as a buffer between the Raj, Russia and Iran.

The Pashtuns on the British side of the Durand Line were never directly governed -- no taxes, no police, no courts. As long as they stayed in the hills and didn't raid the towns, the British left their tribal structure alone and dealt with them diplomatically. When they plundered too much, the Brits sent punitive expeditions to burn a few villages in retaliation, and then things settled back to normal. That's what Pakistan inherited as the Tribal Areas.

Pashtuns in Afghanistan have never stopped hoping to create a Pashtunistan including all Pashtun inhabited territory. The 1919 Anglo-Afghan War was an attempt, in the aftermath of WWI, to do so. If they ever manage it, there won't be much of Pakistan left. The Pakistan government's policy has therefore always been driven by the fear that if Pakistan does not control Afghanistan, the Pashtuns will dismember Pakistan.