The extremists, and the fundamentalist nuclear scientists who dominate Pakistan's nuclear programme, are also furious at Gen Musharraf for accepting demands by the US and the International Atomic Energy Agency to investigate the sale of Pakistani nuclear technology to Iran and North Korea.
Fundamentalism is also growing in the army. After a tip-off by the CIA, at least five army officers were arrested in October for helping al-Qa'eda members in Pakistan's border regions with Afghanistan.
Despite all these threats, Gen Musharraf has always tried to appease the Islamic parties and his half-hearted crackdowns on extremist groups have only been carried out because of inordinate pressure from the Americans.
Until recently the army has allowed extremist groups to continue crossing into Indian Kashmir to battle Indian troops, while the intelligence agencies are turning a blind eye to the resurgent Taliban.
He has also done little to root out fundamentalists in the army's officer corps. His unwillingness to take the fundamentalists seriously is now proving to be a direct threat to his life.