This is a bizarre article. Its author purports to believe that the United States has always offered "friendship" to Muslims (see the first sentence), then points out that the key, 11th paragraph, in the treaty with Tripoli and Algiers was in fact a fabrication, yet this does not prevent the article from ending with the idea that yes, indeed, America always offered friendship that was unreciprocated. The article is wrong, in almost every way, but in any case leaves one confused. .
The real history goes something like this: although the first treaty (of Commerce and Friendship or Friendship and Commerce) signed with a foreign state by the new Republic was with Morocco, prior to 1790, within a few years American ships were being attacked by corsairs (not exactly pirates, for they had official sanction, and would register their intended targets) from Morocco, leading to low-level hostilities. Robert Bove notes further that James Madison took the measure early of the Muslims, and he might have added a whole cast of characters, including William Eaton. Jefferson, John Adams and, especially, John Quincy Adams, who wrote acutely about the nature of Islam, and the hostility to Western Christendom that was prompted by the immutable tenets of the faith (so much for Pipes' notion that "Islam can be whatever Muslims want it to be"), understood the problem.
Indeed, far from being well-disposed toward Islam, "friendly" toward Muslims, Americans throughout the nineteenth century saw the leading Muslim power, taken to represent Islam, that is the Ottoman Empire, and the Ottoman Porte, as decadent, untrustworthy, and violent. American missionaries set out as long ago as 1819 for the Muslim East; they were engaged, unapologetically, on a mission civilisatrice and both the American University in Beirut, and Roberts College in Istanbul, were the fruits of American missionaries who wished to bring learning as well as Christianity to the benighted Muslims. The full story of what these people endured in order to christianize and enlighten the Muslims is a grim one, and they often suffered. Later on these missionaries were witnesses to all kinds of Muslim outrages against Christians: in Damascus, in 1860, against the Maronites, and in 1894-96 the first pogrom against the Armenians, conducted by both Turks and Kurds.
It is only in this century, and almost entirely after World War II, that the understanding -- and consequent mistrust -- of Islam and its adherents began to disappear, as the meaning of that old phrase -- radix malorum cupiditas est -- kicked in, and as so many became, directly or indirectly, hirelings of the Arabs. Combined with that irreducible number of people who, all over the West, are antisemites (as low as 10% of the population in someplaces, as high as 25% in others, or sometimes more in special historical circumstances), and who therefore could be expected, in their publicly-accepted version of antisemitism, anti-Israel vilification, to support the Arabs and make excuses for Islam -- and so they did, and so they are doing still, and in the process becoming as much of a security risk to the survival of the West as were antisemites in Europe and America in the 1930s.
Pipes has it all backwards. The true story is this: many of the most distinguished early figures in American history were not fooled by Islam. They saw it plain. Some of them had negotiated with the rulers of Morocco, Tripoli, Algeria. Others, later, had dealings with the Turks, and observed how the Christian and other non-Muslim minorities were routinely treated all over the Muslim world. And they wrote indignant articles, compiled indignant books. I have one right here -- a collection of testimonies by American missionaries about the abominations of "the Turk" in 1894-96.
Aside from a few discrete episodes -- the Barbary Pirates, and the experiences, direct or indirect, of Jefferson, John Adams, Madison, John Quincy Adams, and then of American missionaries and travellers who were were similarly unimpressed with Islam (why would they be?) and took its true measure, Islam was simply not of much interest either to the American government or to the American people. True, there were accounts, now and again, of those seamen taken prisoner by Muslims. There is the famous tale of Riley and the Brig Commerce, for example. But it was, by and large, the European powers that dealt with the Ottoman Empire, and tried to force upon it changes in the treatment of non-Muslims in its domains. Lincon during the Civil War regarded with alarm the use, by the French, of 500 Muslim troops from Egypt to support Maximilian in Mexico, but that had little to do with Islam. Muslim peoples and polities were not of much interest. to Americans. They had nothing to offer. They were not much of a threat, and Britain, France, and Russia could, in their separate ways, ameliorate the condition of Christians under Turkish rule.
Surely what needs to be impressed upon the consciousnesses, if not the consciences of American would-be statesmen of both parties, that the great figures of American history -- such men as Jefferson, John Adams, Madison, John Quincy Adams--saw Islam plain. The profound effect of oil money and the army of hirelings -- former diplomats, businessmen, journalists, public relations specialists, academics who sit on chairs well-upholstered with Arab money or direct "Centers" of "Islamic Thisandthat" (see John Esposito, see Michael Hudson, both at Georgetown, or see Durham, Exeter, and so many other places where Saudi money rules the cock-a-doodle roost), and the misunderstanding of Islam that results from the takeover of so many academic departments by apologists, both Muslim and non-Muslim, for Islam, has led to the monstrous but widely accepted apologetics, that buttresses, and is buttressed by, the widespread ignorance of Islam and the sappy-sentimentalism ("everyone wants the same thing" which is a degraded variant on that old Catholic staple of bomfoggery -- Brotherhood-of-Man-Fatherhood-of-God -- that stars a priest played by Spencer Tracy or, if he's not available, then possibly Fred MacMurray) that is such a distinctive feature of the age.