'a fundamental misunderstanding of the root of the conflict'

" ... Many historians consider the Barbary wars a sideshow relative to contemporaneous events such as the French Revolution, Napoleon's conquests, and the War of 1812, but the Barbary wars are significant to today's conflict. Franklin, Washington, Adams, Jefferson, and Madison each believed the Barbary wars to be a continuation of the American Revolution. The ground war in North America may have freed the United States from British tyranny, but the Barbary campaign was necessary to win the same freedom of action and commerce within the international community. The episode also crystallized perceptions of Islam and the Ottoman Empire in the American mind. While Americans did not perceive the Barbary wars as a conflict between Christianity and Islam per se, religion was an issue. The two sides fought, not over theological differences, but rather as a result of the divergent ideologies enabled by the two faiths. Washington and Adams referred to the Muslim leaders as "nests of banditti" while Jefferson's and Madison's campaign literature called them "petty tyrants." The "despotic Turk" became the antithesis of early American republican identity.

What Americans and Europeans saw as piracy, Barbary leaders justified as legitimate jihad. Jefferson related a conversation he had in Paris with Ambassador Abdrahaman of Tripoli who told him that all Christians are sinners in the context of the Qur'an and that it was a Muslim's "right and duty to make war upon them wherever they could be found, and to enslave as many as they could take as prisoners." Islam gave great incentive to fighting infidels, Abdrahaman explained, because the Qur'an promised that making war against infidels ensured a Muslim paradise after death. Richard O'Brien, the imprisoned captain of the Philadelphia merchantman Dauphin and later the U.S. consul to Algiers, related similar conversations with ‘Ali Hasan, the ruler of Algiers. Ottoman leaders used the same rationale to justify the enslavement and trading of captives from the Balkans, Caucasus, and Ukraine.

The role that jihadi ideology played in the Barbary wars is documented with explicit references to jihad and holy war in the treaties that U.S. officials entered into with Muslim rulers. Tunis and Algiers, as the western outposts of the Ottoman Empire, even described themselves to American envoys as the "frontier posts of jihad against European Christianity."

U.S. officials took a conciliatory attitude. Realizing that the North Africans were hypersensitive to the historic conflict between Islam and European Christianity, especially in the context of the expulsion of the Moors from Spain, U.S. officials bent over backwards to deny the religious and ideological nature of the conflict, especially to the Muslims themselves. They realized that religious conflict might jeopardize the commerce that the United States still hoped to find in the Mediterranean. In 1821, President John Quincy Adams was barely able to resist assisting the Greeks in their war of independence when both the American and European publics urged war with the Ottoman Empire. The founders possessed a deep conviction for religious tolerance and proudly explained in the short-lived 1797 treaty with Tripoli that the U.S. was not a Christian state at all but rather one which had no official religion and maintained laws forbidding the prohibition of religion. Perhaps their denial of the religious and ideological nature of the conflict foreshadowed the attitude many Washington policymakers adopt today. Then as now, it has become the basis of a fundamental misunderstanding of the root of the conflict. ... "

From Grievance-Based Terrorism By Melvin E. Lee, Middle East Quarterly, 25 Jan 2008