Flood believes the Taliban is a "Pashtun ethno-nationalist insurgency" which leaves out the other tribal groups in the country. Those who refuse to let elements of the Taliban back into the government are mostly non-Pashtuns. Non-Pashtuns made up the Northern Alliance that originally worked with NATO forces to oust the Taliban.
According to the CIA's World Fact Book section on Afghanistan, Pashtuns make up 42% of the Afghani population, Tajiks 27%, Hazaras 9%, Uzbeks 9%, Aimaks 4%, Turkmen 3%, Balochs 2%, other 4%. In other words, Pashtuns are the largest Afghani ethnic group who fall substantially short of a national majority of the Afghani population, but are a clear majority in certain large regions, see this U.S. Army ethnolinguistic map.
The new Afghan constitution gives all Afghanis equal rights, regardless of tribal affiliation. The irreconcilables, as Flood calls them, insist that, to be welcomed back into the fold, Pashtun Taliban must agree to accept the constitution as the national law instead of insisting on a "brutal interpretation of Islamic law at any cost."
By fighting the Taliban the west appears to have been drawn into a tribal conflict of long standing, on the side of the smaller non-Pashtun tribes. Other recent examples of U.S. intervention in tribal conflicts include the Iraq war, the Balkans and Libyan incursions.
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The CIA World Fact Book says Pashtuns make up more than 15% of the Pakistani population, in other words, three Pakistanis out of 20 are Pashtuns. This is one of the reasons Pakistan refuses to join whole-heartedly in NATO's anti-Taliban battle.
I imagine Pakistan fears a drive by "their" Pashtuns to make Pakistani border territories into a Pashtun homeland/nation, much as Turkey fears a drive by Kurds to make eastern Turkey a Kurdish homeland. See a CIA map of the borders of a possible Pashtunistan here.
