Pat Buchanan, in criticizing what he sees as the US' undue focus on the Islamic Middle East, frequently points out that Pakistan is one bullet away from a nuclear-armed, Islamic-led nation of 160 million people, nearly half of whom have a favorable impression of Osama bin Laden.
Bhutto's assassination underscores as much. Given the successive attempts on her life, it seemed irresponsible for her to continue to invite attacks that could (and would) lead to the deaths of hundreds of her supporters. It also suggests that, to say the least, opening up Pakistani society at this point would be destabilizing. Bill Richardson's call for Musharraf to step down is a call for chaos (and Joe Biden's excoriation of that position confirms in my mind that he is the best Democratic Presidential candidate being fielded).
In Bhutto's defence, she had requested foreign protective services, for which she had offered to foot the bill. Musharraf apparently scoffed at the idea, insinuating that his government could protect her.
While Bhutto was a liberal by the standards of the region, especially in the area of women's rights, she was hardly a reliable friend of the US. It was while she was prime minister that the Taliban moved from Afghanistan's southwest into the seat of that nation's power. Though some elements of the ISI despised her in the mid-nineties for not being supportive enough of the Taliban (and may well be revealed to have had some role in killing her a decade later), her support and recognition of the group was crucial to its rise to power.
Randall Parker has a great post on the former Pakistani prime minister.