I think Daniel Pipes (as good scholar as he is) also misreads Islam.
Muhammad himself was a ruthless warrior bringing Islam to Arabian Penninsula by sword. He is responsible for the destructions of the Jewish Communities in Medina and other places. His successors, like Timur Tamerlane, Saladin, Sultan Mehmet, etc. are well known for their ruthless plunder and systematic destruction of infidels. If Al-Qaida, Hamas, etc. violate Koran on the rules of warfare, than the founder of Islam is violator too. It's a misconception that modern day Islamic terrorists hijacked Islam. They are in fact following the precepts of Koran, Sunna and Hadith, so Daniel Pipes is clearly wrong here.
The catch is who decides who is innocent and who is not. For Jihadists, all "infidels" (non-Muslim) are guilty till they convert to Islam, submit to Islamic rule to live as Dhimmi (to live as "protected" discriminated minority in Islamic country payment of special taxes on non-Muslims, prohibition to worship publicly your religion, etc.).
Again, too many Western Scholars did not study Islamic theology and history hard enough to see that Traditional Islam is the source of terrorism and they were duped by Islamic propaganda that Traditional Islam is "Religion of Peace", etc. Nothing can be further from the truth and 1400 year history of Islam shows plenty of examples of those.
Here is a good post on FR summarizing 1400 of Islamic Jihad. I posted the last section here. Islamic Terrorism Is it a New Threat?
The bottom-line is that Islamic terrorism that we see today is not a new phenomenon. It has occurred continuously since the 7th century institution of the Islamic faith. The only difference is that throughout the Islamic history, the onus of terrorizing the non-Muslims were undertaken by the Islamic states. The ferocity, destruction and violation have been of much greater scales in the Islamic rulers devastating attack of innocent infidel territories and out-posts, slaughtering both military and civilian population (mainly men) in tens of thousands, enslaving their children and women in great multitude and destroying their religious institutions and forcing them to conversion. The present scourge of terrorist atrocity is virtually negligible as compared to those unleashed by the Islamic rulers on the infidels throughout the Islamic history. Just because the tentacles of Islamic terrorism have reached the Western world it has become such a hype in the last few years post-9/11.