David Barton, pseudo-historian (and dolt), will soon be publishing The Jefferson Lies, wherein he tries to demonstrate that Thomas Jefferson was just as much of an evangelical, miracle-believing, Jesus-praising, conservative Christian as … well, Dave Barton claims to be.
Part of the debate is Jefferson's Bible. The first was an abridged version, with various teachings and events clipped from the Bible by Jefferson and organized by theme. The second (which survives – http://books.google.com/books?id=AmAJAQAAIAAJ) was an abridged version of the Bible with all the supernatural bits trimmed off.
How does David Barton somehow turn this into proof of Thomas Jefferson as Bible-thumping evangelist who would doubtless support Rick Santorum, et al., as candidates for the White House? Well, he doesn't do it honestly …
(See also http://www.rightwingwatch.org/content/david-bartons-outrageous-fabrication-about-thomas-jefferson and http://wthrockmorton.com/2011/04/12/was-the-jefferson-bible-an-evangelism-tool/ ) #ddtb
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Jefferson's Bible
Rick Santorum 's near-miss in Iowa provides a reminder that, for many Republican voters (and not a few candidates), religion and politics overlap. If you need another reminder, though, consider this: …
As an evangelical Christian, I have no problem accepting the fact that Jefferson, Franklin, Adams, and probably Washington had religous beliefs that are significantly different from my own. You have to wonder how some of these people who talk about the "Christian Founding Fathers" would react if one of them actually applied for membership in their OWN church.
I wonder how David Barton deals with the book that Keith Ellison used to take HIS oath of office.
I don't understand why some folks require the Founders to all be in lock-step ideologically, in particular with their own ideology. Well, actually, I do understand it, but it's a simplistic view of the world that ends up promoting dishonesty to twist reality to meet your needs (see: David Barton).
Barton's commentary on Keith Ellison's swearing in can be found at http://www.wallbuilders.com/downloads/newsletter/Winter2006.pdf … it's a veeeeeeery long document (with a rather slanted review of the history in the link you provide), but it basically boils down directly what you'd expect: MUSLIM = UN-AMERICAN = EVIL.
While I doubt that Jefferson drew particular inspiration from the Koran, he bore no specific hostility to Islam. He was proud that the Virginia Act for Religious Freedom did not explicitly protect just Christians, but that it covered "within the mantle of its protection, the Jew and the Gentile, the Christian and Mohammedan, the Hindoo and Infidel of every denomination".
The article you cite gives a very loose and popular overview of the "Shores of Tripoli" campaign against the Barbary Pirates. I'd whole-heartedly recommend The Pirate Cost by Richard Zacks for more about the Barbary Pirates and the Marine expedition somewhat inadvertently sent against them (and the less than stellar results).
Speaking of Keith Ellison, Ellison has been accused of painting as false a picture of Jefferson as Barton has http://voices.yahoo.com/refuting-congressman-keith-ellisons-claims-thomas-165998.html
It's also worth noting that Jefferson obtained his Koran (the one Ellison was sworn in on) in 1765 as part of his research into natural law and religious history — which is a fuzzy, less exaggerated versionof what Ellison was claiming. Barton, for one, conflates this with an episode twenty years later when the Ambassador of Tripoli justified the Barbary attacks on Christian shipping as religiously driven (just as self-serving as Christian slavers in Africa claimed conversion of the natives to Christianity was their excuse for buying slaves), and that Jefferson picked up a copy of the Koran then to research proof of the claim.