The Founders' Original Problems with Islam Didn't Prejudice Them:

Chuck Norris' recent column for WorldNetDaily brings to mind an irony: Folks hostile to Islam, have, of late, pointed out America's problems with Islam are nothing new and point back to America's founding era where the Barbary pirates, notably during the Adams and Jefferson Administrations, targeted European and American ships for looting and enslavement. As the story goes, the Muslim pirates felt the Americans' and Europeans' Christian or non-Muslim religion justified the attacks. I've scoured the Founders' writings on Islam, and despite those problems, it did not lead Jefferson or Adams (or any of the other notable founders for that matter) to conclude there was anything in principle wrong with the Islamic religion. On the contrary, from what I've been able to glean, Adams and Jefferson thought Islam analogous to Christianity: It was a religion that was at heart true (because it, like most other religions, taught there is an overriding Providence and future state of rewards and punishments) but had been corrupted by dogma.

Here is Adams, well after retiring from the Presidency on Islam:

“It has pleased the Providence of the first Cause, the Universal Cause, that Abraham should give religion not only to Hebrews but to Christians and Mahomitans, the greatest part of the modern civilized world.”

-- John Adams to M.M. Noah, July 31, 1818

And here is Jefferson who draws an equivalence between the bloodshed in Christianity and Islam while noting all religions (presumably including Islam) are valid:

Every religion consists of moral precepts, and of dogmas. In the first they all agree. All forbid us to murder, steal, plunder, bear false witness &ca. and these are the articles necessary for the preservation of order, justice, and happiness in society. In their particular dogmas all differ; no two professing the same. These respect vestments, ceremonies, physical opinions, and metaphysical speculations, totally unconnected with morality, and unimportant to the legitimate objects of society. Yet these are the questions on which have hung the bitter schisms of Nazarenes, Socinians, Arians, Athanasians in former times, and now of Trinitarians, Unitarians, Catholics, Lutherans, Calvinists, Methodists, Baptists, Quakers &c. Among the Mahometans we are told that thousands fell victims to the dispute whether the first or second toe of Mahomet was longest; and what blood, how many human lives have the words ‘this do in remembrance of me’ cost the Christian world!... We see good men in all religions, and as many in one as another. It is then a matter of principle with me to avoid disturbing the tranquility of others by the expression of any opinion on the [unimportant points] innocent questions on which we schismatize, and think it enough to hold fast to those moral precepts which are of the essence of Christianity, and of all other religions.

-- Thomas Jefferson to James Fishback, Sept. 27, 1809.

Finally, here is an informative page from James H. Hutson and the Library of Congress noting how much public opinion of Islam during the founding era was positive.