See this for detailed background on U.S. relations with Pakistan, including links to Afghanistan, Taliban, nuclear proliferation, Kashmir, China-India relations, the supply of suicide bombers, bin Laden ... Whew! What a mess!
Pakistan is one of Bush's major fronts in his war on terror, although he hasn't acknowledged it. The war there is clearly not going his way. While many terrorists have been captured, many more have been recruited, they have a base of operations, they have bloodied the nose of Pakistan's military, and they have rebuilt and regrouped.
Who in his administration thought that Bhutto could survive and become a new U.S. puppet in such an environment? It was a very bad bet.
The U.S. originally linked with Pakistan in the 50's because of the Soviet Union. The excuse now is terrorism. This Islamic country became a socialist mess with nuclear weapons.
Why are we so involved with Pakistan? Fortress America does not seem like such a bad idea.