In part the confusion is an honest and long-standing uncertainty due to the fact that in addition to Jefferson, both John Adams and Benjamin Franklin helped to forge the final version of the Declaration of Independence that was ratified by the Continental Congress on July 4, 1776. And in addition to Jeferson, Adams and Franklin there were also two lesser known members of drafting committee: Roger Sherman, and Robert R. Livingston.
But Walter Isaacson has greatly exacerbated this honest uncertainty by stupidly declaring, in his biography of Benjamin Franklin, the following:
Franklin made only a few changes, some of which can be viewed written in his own hand on what Jefferson referred to as the "rough draft" of the Declaration. (This remarkable document is at the Library of Congress and on its Web site.) The most important of his edits was small but resounding. He crossed out, using the heavy backslashed that he often employed, the last three words of Jefferson's phrase 'We hold these truths to be sacred and undeniable' and changed them to the words now enshrined in history: 'We hold these truths to be self-evident.'"The only people who agree with Isaacson on this issue are those who rely exclusively on Isaacson as their only source on the question. Everyone who has done independent research on the matter is either meticulously equivocal, or tends toward the accepted attribution of the words to Jefferson.
"Possibly it was Franklin, or Jefferson himself, who made the small but inspired change in the second paragraph. Where, in the initial draft certain 'truths' were described as 'sacred and undeniable,' a simpler, stronger 'self-evident' was substituted."
[David McCullough, John Adams, p. 122. Look here for a much longer excerpt of the relevant passage in McCullough.]
"The phrase 'sacred & undeniable' was changed to 'self-evident' before Adams made his copy. This change has been attributed to Franklin, but the opinion rests on no conclusive evidence, and there seems to be even stronger evidence that the change was made by TJ or at least that it is in his handwriting."Pauline Maier, in her "American Scripture: The Making of Declaration of Independence" simply says "the phrase is perhaps Franklin's". [p. 136]
[Boyd, Declaration of Independence, 1945, p. 22-3." (link)]
Carl Lotus Becker, in his 1922 classic The Declaration of Independence: A Study on the History of Political Ideas, states that in his opinion the phrase "self-evident" was already in place before Benjamin Franklin had seen the working draft:
"Jefferson first wrote 'we hold these truths to be sacred & undeniable.' In the Rough Draft as it now reads, the words 'sacred & undeniable' are crossed out, and 'self-evident' is written in above the line. Was this correction made by Jefferson in process of composition? Or by the Committee of Five? Or by Congress? There is nothing in the Rough Draft itself to tell us. As it happens, John Adams made a copy of the Declaration which still exists. Comparing this copy with the corrected Rough Draft, we find that it incorporates only a very few of the corrections: one of the two corrections which Adams himself wrote into the Rough Draft; one, or possibly two, of the five corrections which Franklin wrote in; and eight verbal changes apparently in Jefferson’s hand. This indicates that Adams must have made his copy from the Rough Draft when it was first submitted to him; and we may assume that the eight verbal changes, if in Jefferson’s hand, which we find incorporated in Adams’ copy, were there when Jefferson first submitted the Draft to Adams — that is, they were corrections which Jefferson made in process of composing the Rough Draft in the first instance. With Adams’ copy in hand it is therefore possible to reconstruct the Rough Draft as it probably read when first submitted to Franklin."
[Chapter Four: Drafting the Declaration: link]
This is a case where there is room for some small amount of reasonable doubt. But there is in fact very little evidence against the traditional and accepted attribution of the phrase "We hold these truths to be self-evident" to Thomas Jefferson.