The Afghan government believes that al Qaeda is not present in Afghanistan in any significant numbers. Foreign military commanders, often advised by U.S. Army Special Forces operators who have been working in the country since late 2001, tend to agree. Al Qaeda's problem in Afghanistan is that they are greatly disliked. This all goes back to the early 1990s.
Back then, the Taliban were out to establish a religious dictatorship in Afghanistan . The one flaw in this plan was that the Taliban enforced Islam as interpreted by a few the Pushtun tribes in southern Afghanistan. The Pushtuns were only 40 percent of the population, and the Pushtun tribes the Taliban came from, were a fraction of that. Resentment began to build so that by the late 1990s most Afghans hated the Taliban. In addition, non-Pushtuns in northern Afghanistan (the Northern Alliance) continued fighting the Taliban. Fortunately for the Taliban, they had given Osama bin Laden, and his al Qaeda organization, sanctuary in 1994. Bin Laden arrived as the Taliban were still in the process of fighting for control of most of Afghanistan. From the beginning, al Qaeda provided the Taliban with technical support, and gunmen who were more ruthless and deadly than your average Afghan warrior. By the late 1990s, the al Qaeda brigade was a principal means of enforcing Taliban rule in many parts of the country.
But for seven years, al Qaeda had a place to set up shop. This included training camps, support activities and a safe place for terrorists to rest up between missions. The training camps were out in the hills, but many senior al Qaeda officials hung out in Kabul and other cities.
By the late 1990s, the Taliban were becoming increasingly unpopular because, basically, the Taliban represented the religiously conservative Pushtun tribes of southern Afghanistan. Unlike previous Afghan governments, the Taliban were not interested in working out deals. You did things their way, or they sent their brigade of al Qaeda gunmen to straighten you out. The use of the foreigners as enforcers was the last straw for most Afghans. The al Qaeda brigade was composed mostly of foreigners (mainly Arabs). The Arabs were contemptuous of the Afghans, whom they viewed as a bunch of ignorant country bumpkins, and the Afghans picked up on this.
Afghans have not forgotten the treatment they received from the al Qaeda foreigners, and this hostility was ramped up when al Qaeda brought in their suicide and roadside bomb tactics to Afghanistan five years ago. This was a tactic al Qaeda believed was leading them to victory in Iraq, and would repeat that success in Afghanistan. The bombing tactics, which killed so many civilians, ultimately failed in Iraq, and is having the same impact in Afghanistan.
The only Afghans who get on well with al Qaeda are the Taliban leadership (or at least some of them). Most of these men, and nearly all al Qaeda members, fled to Pakistan after 2001. Some have returned, but the al Qaeda who came back found that most Afghans still hated them. Al Qaeda made itself unpopular among the Pakistani Pushtuns as well, and this led to some battles that left hundreds of al Qaeda men dead. Al Qaeda has since learned to behave better in Pakistan, and that's where the remaining al Qaeda bases are. But al Qaeda has a tenuous tenure in Pakistan, and none at all in Afghanistan.