2 reasons why not all Muslims are terrorists.

In short, there are two reasons that not all Muslims are terrorists. First, not all who label themselves a Muslim are a true Muslim (just like not all who label themselves a Christian are a Christian). Second, this sixth pillar is an obligation on the entire community of Muslims and not each individual.

If you do find a Muslim who condemns the terrorists then pay close attention to their words. The Muslim will point out that it is wrong to kill civilians or those who are not at war with Muslims.

On the other hand, they never condemn the objectives of the terrorists because you cannot refute the objective using the Qur'an. It is the duty of the community of Muslims to destroy every non Muslim government and replace it with an Islamic government (khaleefah). Read and you will understand.

To a real Muslim, the question is not "should the United States government be destroyed?" but "have the residents of the United States been sufficiently called to Islam?" because all the scholars agree that Muslims are not allowed to fight the enemy unless they are called to Islam in the first instance. In other words good Muslims do not fight their enemy without first offering the enemy a chance to accept Islam.

If this offer is turned down, they are asked to pay 'Jizya' (head tax), and to be part of the State and be ruled by Islamic Shari'a. If the enemy (like the United States) refuses both options, Islam or Jizya, then the Muslims are allowed to declare war on them (and fly planes into buildings).

http://www.notislam.com/id8.html