Time lines and events at that point of time is very important to form a proper view. They were allied because of the simple single objective : Soviet Union.
I am talking post-Soviet Afghanistan. All those famous Pashtun commanders of the Soviet war, actually joined with the rest of the Mujahideen in their war against the Taliban and Pakistan. I am talking solely post-1992,
not the Soviet war.
The enemy of my enemy. Northern Alliance is a predominant minority led opposition, it is still not Afghan nationalist in the true sense. There is no such entity in afghanistan.
Northern Alliance only came into being in 1996, after the Taliban, with Pakistani assistance had already forcibly taken over majority of the country. Pre-1996 (and post-'92) all the original Mujahideen Pashtun commanders were united with the rest of the Mujahideen in their war
against the Taliban. The commanders I mentioned from the Soviet war; Agha Sherzai, Abdul Rasul Sayaf, Abdul Haq, Haji Abdul Qadir, Abdul Rahim Ghafoorzai and countless other major Pashtun Mujahideen commanders were all united under Burhanuddin Rabbani leading the Islamic State of Afghanistan, and fought
against the Taliban. They were either taken over and killed by the Taliban, or they dispersed to the North. Unlike the Taliban, which had explicit Pakistan army support, these chaps were fighting with their backs to the wall, with little outside support.
Since there is only one Pashtun faction that holds power, that is the Taliban. Therefore Taliban is the legitimate representatives of the pashtuns as long as they hold territory and power. whether we like it or not , is another matter.
Errrmm noo, there were/are other Pashtun factions which opposed and fought the Taliban. Ittihad-i Islami being a major one. There were many others, Haji Abdul Qadir, Agha Sherzai, and heck there were even many initial Pashtun Taliban supporters who switched sides and started to support the Northern Alliance against them, Hamid Karzai being a famous one. Saying that Taliban represented all Pashtuns, is like saying the British Raj represented all Indians.