"Bush was criticized. . . for applauding the overthrow of the democratically elected Nawaz Sharif government in the Oct. 12, 1999, military coup. His spokesperson at the time, Karen Hughes, said that Bush was encouraged by Musharraf's promise that he would hold early elections, restore "stability" to Pakistan, and ease tensions between India and Pakistan. . . What the world did not then know was that President Bill Clinton had negotiated a deal not long before with Prime Minister Sharif whereby Pakistan would deploy special operations troops to capture Osama bin Laden. When Musharraf took power in fall of 1999, he refused to honor the deal, since the operation was unpopular with the military's fundamentalist officers. Indeed, Bush was supporting a man who derailed the best chance the Clinton administration may have had to prevent Sept. 11." [Musharraf's power grab in Pakistan | Salon.com]
In all fairness to Bush (can't believe I'm typing those words), he couldn't have known about the deal President Clinton had made with P.M. Sharif and it is only in hindsight that you ache for the lost opportunity. The primary focus of the Salon article is to describe Bush's continued support for Musharraf because we continue to need his help, apparently even more than Musharraf needs the billions of dollars we've given his country in aid.