The Pushtun civil war, on both sides of the Afghan-Pakistan border, has cost Afghanistan billions of dollars in additional transportation costs, and lost or damaged cargo. That's because Afghanistan is landlocked, and most imports and exports move along the 1,600 kilometers long truck route from Kabul to the Pakistani port of Karachi. Only a few hundred kilometers of the route (mostly National Highway 55 in Pakistan) is a proper, multilane road common in the west. The rest of it, especially in the Pushtun territories astride the border, is a poorly maintained and quite narrow two lane road, often twisting its way up and down mountains.
For centuries, the tribes along this route collected payments from the merchants (or, these days, trucking companies) to insure safe passage. Some of the current tribes are pro-Taliban, but this is business, and it has become more lucrative as the Afghan economy has revived since 2001 (when the reactionary, and bad for business, Taliban were chucked out). But as the Pushtun tribes split into pro and anti-Taliban groups, one of the side effects was a struggle over who would control the "security" business on the roads into Afghanistan. This explains the growing number of attacks made on convoys and truck stops. While you hear about the U.S. and NATO convoys being attacked, the battles back in the hills, between the rival warlords, gets less coverage (mainly because reporters are apt to be shot, just to keep the media away from the savage fashion in which these disputes are settled.) The truck security payments (often a thousand dollars or more per truck per trip) are a major source of cash for the border tribes. It's something worth fighting, and dying, for. In the last five years, the cost of getting a truckload (usually just a large cargo container) from Karachi to Kabul has gone from a thousand dollars to nearly $3,000. In the process, over 5,000 trucks were destroyed and at least 120 drivers killed. But only about one percent of NATO shipments have been lost.
While religion and tribal politics play a big role in the Taliban and al Qaeda violence in Pakistan and Afghanistan, you also have to follow the money to get to the source of most of the fighting. You can live without religion, but you can't live without food. And that will cost you, especially in one of the poorest regions of Asia. It's also one of the most heavily armed parts of Asia, where hungry tribesmen have long resorted to violence when they were hungry, or just greedy.
U.S. and NATO commanders soon got fed up with the "protection" scam being run them on the supply route. The tribes that live along the road expect to be paid, as do the criminal gangs near the dozen truck staging areas (where shipping container are loaded). Some 50,000 of those containers a year carry U.S. and NATO military supplies, and over 500 trucks carrying NATO supplies move along this route each day. That's about half the traffic, which has increased greatly since the Taliban were tossed out of power in late 2001. Getting each container from the Pakistani port of Karachi to Kabul costs several thousands of dollars in fees, bribes and wages to Pakistanis, Afghans and assorted greedy officials and tribesmen along the way. Some tribal leaders say they are only interested in keeping the trucks from bringing alcohol and pornography into Afghanistan, but the bottom line is how much cash gets into the pockets of some of the gunmen living along the route.
In response, NATO has been bringing more cargo in via Russian and Central Asian railroads (the old Soviet rail network). This has been increasing over the last two years, and is making a noticeable dent in traffic going through the Khyber pass. That means most of the traffic being threatened now is for the Afghan economy. Thus more civilian traffic is also shifting to the rail lines coming to the Afghan border via Central Asia. For the first time, some railroads are being built in Afghanistan. But until the Pushtuns settle their civil war, the country will be too dangerous for an extensive rail network. In fact, that Pushtun chaos is why there has never been a rail network in Afghanistan.