The Pakistani military establishment, which spawned Musharraf, has a record of using Islamic fundamentalists as tools --- both in Afghanistan, where they were largely responsible for maneuvering the Taliban in to power, and in Kashmir, where they have supported the terrorist groups which have a long record of terrorist acts, and most recently, disrupted Kashmiri local elections. And in the Pakistani elections, Musharraf went out of his way to do favors for the Islamic parties, effectively exempting them from a requirement that candidates have a college eductation (by giving them full credit for certificates from madrassas), while at the same time trying hard to prevent the established secular parties of Benazir Bhutto and Nawaz Sharif from fielding candidates. (To be fair, Musharraf would complain that both secular parties are deeply stained by corruption, and he's right. But he has done little or nothing to build up a credible secular alternative, while going out of his way to help the Islamists).
In short, the Islamists are in the Pakistani parliament because Musharraf wants them there, and because he prefers them to advocates of secular, modern governance. If that starts to give you the creeps about the guy, you might want to take a look at Ahmed Rashid's overview of the Pakistani scene just before the elections. That'll make you really scared.