Militant Salafism is the root of the problem

'The current situation in the Pakistan-Afghanistan region has been largely shaped by the Pakistani army's support of militant organizations over the past three decades. This ongoing support is rooted in the Pakistani identity and in Pakistan's perception of its role as an Islamic state ever since its creation in 1947.

For more than half of its 62 years, Pakistan was ruled by military officers. But even when it was ruled by civilians, in the debate over Pakistan's identity, secularists and liberal forces have always lost, while the military and the religious groups have always set the nation's agenda and defined its future course.[1] The way the Pakistani leaders view their identity defines their domestic policies and foreign relations. The shaping of the Pakistani identity on the Islamic path has over the years turned Pakistan into an expansionist state, which has translated into the military's policy of "strategic depth." In practical terms, this policy meant a constant concerted effort by the military-led Pakistani establishment to go beyond its borders into India (not only in Kashmir but also the mainland India) and in Afghanistan through the use of militant groups.

This self-perception of Pakistan's role, responsibility and identity is a genie that has been out of the bottle for decades now, and there is no way to get it back in. It has become the most decisive factor in the region's history and politics – so much so that when Pakistani military ruler General Pervez Musharraf tried after September 11 to reverse, though reluctantly, the policy of using the militant organizations as "strategic assets," he was not able to do so. In fact, this genie is so strong now that a number of young militant leaders who have emerged in recent years and are more ideologically driven are now beginning to launch attacks on the Pakistani security institutions, particularly since the military began cooperating with the U.S.'

PS: It's amazing how quickly a post ends up on Google. Just a few seconds after I posted the above I googled militant salafism and found this concise analysis:

"The militant Salafism that began in 1980s took the simple nature of Islam and added the notion of militancy from the Qutbi current (after Sayyid Qutb). The combining of Qutbism and Wahhabism took place in Afghanistan through Ayman al Zawahiri and Osama bin Laden, where the walaa and baraa equation met with Sayyid Qutb's theory of divine governance that denounced contemporary society as infidels.

The takfiri Qutbi current utilized the physical potentials of the scholastic Salafism and turned toward militancy."