The main Afghan foe of the Taliban was the Northern Alliance, long backed by the Russians, and more recently backed by both the Russians and the USA. The Northern Alliance were also the main people behind the opium trade during the rule of the Taliban (who were considered friends of America until shortly before 911), because the Taliban attempted to eradicate the opium trade (for purely religious reasons). In doing so, needless to say, they made a lot of local enemies because the opium trade is almost the only viable way for the rural people to make a living in Aghanistan. The Northern Alliance have been the main people to benefit from the ouster of the Taliban, and they are strongly backed by both Russia and the USA now, which is a bit ironical, I think... ;-) The Russians like them because they are leftists and they're helping the Russians fight Islamic fundamentalist groups in that region. The Americans like them because they are fighting the Islamic fundamentalist groups, period...and they're not the Taliban. Both Russia and the USA want the Taliban eliminated.
The Pakistanis hate the Northern Alliance because the Taliban were proteges of the Pakistani ISI which was looking to keep the Russians permanently out of Afghanistan and saw the Taliban as the way to do it.
But America gave Musharaff an ultimatum back in 2001...either abandon the Taliban and help us destroy them or we will destroy you. Musharaff knuckled under. He had really no choice, but his army and population felt betrayed (which they were), and it ruined their entire longterm strategy for that region.
I mention none of the above to prove that the Taliban are "good guys". ;-) They're not. And neither are the Northern Alliance. I mention it merely to show how infernally complicated the situation there is. It's been an utter disaster for both Pakistan and Afghanistan...and ultimately not any good for the USA either.