Yes, most Pakistani's are Muslim, there's a very small minority of Hindus, Zororastrians, and Christians there. They are protected by the constitution, though. One of the best cricketers in the world right now converted from Christianity to Islam last year or year before. He was Yousuf Youhanna and now he's Mohammed Yousuf. His parents are still Christian.
Benazir Bhutto was president of Pakistan from like 1989 to 95 or 96. As long as she was dressed modestly, they didn't have a problem with her (as a woman) leading them. There have been other Muslim women leaders - not many, but there have been others around the world. She was not squeaky clean, either. Don't forget that the Pakistani Inter-Services Institute funded the formation of Afghanistan's Taliban in 1993 and 1994 - when she was president. The ISI is one of Pakistan's intelligence services. One spys just on India. Another watches internally, and the ISI watches both of them. The ISI also has the Afghan desk which "interferes" in Afghanistan (according to the Afghans of all stripes). Then there's Military Intelligence which watches everybody else.
If you check this new movie, Charlie Wilson's War and the book and the History Channel documentary about the actual events behind the movie, all of the Pakistani's are ISI Afghan department. The United States and Saudi Arabia spent something like $6 billion dollars through ISI Afghan desk to fund the war against the Communist Afghan government from 1979 to 1989.
Musharraf is the head of the military and is a dictator. He siezed power in 1999 and manipulated the system to get a nomination for president in next month's democratic elections. By the way, I''ll bet my last dollar this is Al Qaida. They do things in twos. They want Bhutto dead, they want Musharraf dead, and they want the other main candidate Nawaz Sharif dead.