Two things that affect this story were already in place before Bush Jr took office. The first: an already high level of anti-American feelings in the Islamic world, for the years of oil-biased foreign policy. Oil bias is easily perceived as anti-Islam because most of the world's oil is under Muslim countries. The second: plans were already in place for a massively profitable oil pipeline proposed to run through Afghanistan. An uncooperative Taliban had put the brakes on the plan. These two things and how they tie into Bush's War on Terror have become a conspiracy theorists wet-dream.
Anti-Americanism had been bubbling away since the 60's, mostly over American support for Israel's annexation of Muslim land. American foreign policy from the early 80's onwards accelerated the growth of anti-Americanism by an enormous factor. America didn't help itself by arming and heavily funding the extremist of extreme Mujahideen groups as they fought the Soviets in Afghanistan, before cutting all contact and funds when the Soviets withdrew, allowing the country to fall deeper into civil war.
During this era Osama Bin Laden first came to light as a Mujahideen fighter in Afghanistan. His status as a member of a rich Saudi family made him an ideal candidate to secure funds from wealthy Arabs for the Jihad. It is alleged the U.S. pressured Saudi intelligence to hire bin Laden in such a role.
At the same time as giving these "freedom fighters", as Reagan called them, the best weaponry and getting the S.A.S to give them training in building improvised explosives, the U.S, along with many European states was also heavily funding and arming another extremist: Saddam Hussein, in his war with Iran. This led to Saddam becoming, or at least feeling he had become a considerable military power and gave him the wherewithal to invade Kuwait. This led to the U.S. stationing troops in Saudi Arabia, which again stirred the hornet's nest of anti-Americanism in the Islamic world.
By this time the war with the Soviets was over and Osama Bin Laden, now leader of Al Qaeda had left Afghanistan and was moving from country to country, spreading the word and filling the pockets of Jihad. In 1996 Osama Bin Laden issued his first and least menacing religious ruling (fatwa). Calling for attacks on American forces occupying the land of the two holy places, referring to Saudi Arabia and the two Muslim shrines at Mecca and Medina.
Osama returned to Afghanistan in 1998, given refuge by the sympathetic Taliban, who had grown up alongside his Mujahideen brothers in Pakistan's seminaries. His second Fatwa was released the same year, along with Ayman Al Zawahiri (recruited by Bin Laden for the Afghan struggle in the 80’s) leader of the Jihad group in Egypt, and the leaders of three other Islamic extremist groups: The Islamic Group, Jamiat-ul-Ulema-e-Pakistan, and the Jihad movement in Bangladesh. The ruling, in short called on all Muslims to murder Americans (troops and civilians) whenever and wherever in the world they could.