Check out this good article that explains the differences between Iraq and Afghanistan. Just keep in mind that although Baathists are moderate compared to the Taliban, the hardcore Baathists have murdered many innocent Iraqis. And the Saudi radicals may have been interested in striking primarily at coalition forces, but most of their victims have been Iraqis.
From the article:
* The Iraqi malcontents comprised an assortment of the disaffected--secular Baathists, Sunnis suddenly deprived of long-held privilege and power, simple religious bigots (rather than committed doctrinal fanatics, and there is a difference), and, to be honest, Iraqis who merely resented the 2003 intervention. Notwithstanding Beltway blather denying its existence--some emitted by now vice-president Biden--an Iraqi national identity, however limited, exists.
* The Sunni Awakening was encouraged when the Iraqis found their alleged "resistance" increasingly dominated by Saudi Wahhabis who had come over the long Saudi-Iraqi border in the "second Iraq intervention," as detailed here, here, and here. When "Al Qaeda in Iraq" manifested its Taliban characteristics--executing women caught without covered faces, possessors of music CDs, Sufis, and others they deemed apostates--the anti-coalition combatants perceived that the United States and Baghdad authorities were a preferable alternative to governance by lynching.
Wide as the horizons of their global ambition doubtless were, and dedicated as they were to using Iraq as a platform for reinforcement of Wahhabism in their own country, the Saudi radicals who streamed north were primarily interested in striking at the coalition, to stimulate new support for their perverse cause, and did not aim at immediate expansion into Jordan or Kuwait.
By contrast, the Taliban is not a mélange. They include no secular types comparable to the Baathists and few "Afghan patriots." Afghan national identity is much weaker than that found even in Iraq. The Pashtun base of the Taliban is tribal, but they have a lesser presence in local history than the Iraqi Sunnis that usurped power in Mesopotamia. The Taliban embody monolithic radicalism in the Wahhabi style, rooted in the Deobandi school of fundamentalism, and consider all Muslims who fail to share their ideology to be unbelievers deserving liquidation. The Iraqi Arab Sunnis, even at the height of their influence under Saddam, could not wipe out the Iraqi Shias or the Kurds, but the Taliban massacred the indigenous Hazara Shias in Afghanistan, effecting a nearly-successful genocide.
Further, the Taliban have demonstrated that their current goal, rather than mere power in Afghanistan, is the "Talibanization" of Pakistan, a nuclear-armed failing state. This would provide the running dogs of al Qaeda with unconcealed weapons of mass destruction as well as millions of fresh foot-soldiers in an environment that, along with its large and problematical diaspora in Britain, has become the main breeding ground of Islamist extremism worldwide. '