Pakistan is important to US security. It is a nuclear power. Its military fostered, then partially turned on the Taliban and al-Qaeda, which have bases in the lawless tribal areas of the northern part of the country. And Pakistan is key to the future of its neighbor, Afghanistan. Pakistan is also a key transit route for any energy pipelines built between Iran or Central Asia and India, and so central to the energy security of the United States.
The military government of Pervez Musharraf was shaken by two big crises in 2007, one urban and one rural. The urban crisis was his interference in the rule of law and his dismissal of the supreme court chief justice.
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The rural crisis was the attempt of a Neo-Deobandi cult made up of Pushtuns and Baluch from the north to establish themselves in the heart of the capital, Islamabad, at the Red Mosque seminary. They then attempted to impose rural, puritan values on the cosmopolitan city dwellers. When they kidnapped Chinese acupuncturists, accusing them of prostitution, they went too far.
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Most Pakistanis did not rally in favor of the Neo-Deobandi cultists, but to see a military invasion of a mosque was not pleasant (the militants inside turned out to be heavily armed and quite sinister).
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The NYT reported that US Secretary of State Condi Rice tried to fix Musharraf's subsequent dwindling legitimacy by arranging for Benazir to return to Pakistan to run for prime minister, with Musharraf agreeing to resign from the military and become a civilian president. When the supreme court seemed likely to interfere with his remaining president, he arrested the justices, dismissed them, and replaced them with more pliant jurists. This move threatened to scuttle the Rice Plan, since Benazir now faced the prospect of serving a dictator as his grand vizier, rather than being a proper prime minister.
With Benazir's assassination, the Rice Plan is in tatters and Bush administration policy toward Pakistan and Afghanistan is tottering.