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Then there’s the weird atheist insinuation that Jefferson’s reference to “Nature’s God” was a tacit rebuke to Christianity, of which, they claim, the founder was highly-critical.

If you take Christianity to be a religion that believes Christ is God, then TJ was indeed highly critical of Christianity.

He even edited the Bible to take out all references to Christ as God (not that there are all that many of those), to the Virgin Birth, and to the performance of miracles.

http://www.angelfire.com/co/JeffersonBible/

I read somewhere that the "Jefferson bible" was where he cut out all the things Jesus said, pasting them into a blank book, to make a compact book out of it.

In fact, from the very site you posted is this in the introduction:

Thomas Jefferson wrote in a letter to William Canby, "Of all the systems of morality, ancient or modern, which have come under my observation, none appear to me so pure as that of Jesus." He described his own compilation to Charles Thomson as "a paradigma of his doctrines, made by cutting the texts out of the book and arranging them on the pages of a blank book, in a certain order of time or subject. A more beautiful or precious morsel of ethics I have never seen." He told John Adams that he was rescuing the Philosophy of Jesus and the "pure principles which he taught," from the "artificial vestments in which they have been muffled by priests, who have travestied them into various forms as instruments of riches and power for themselves." After having selected from the evangelists "the very words only of Jesus," he believed "there will be found remaining the most sublime and benevolent code of morals which has ever been offered to man."

Jesus himself ha something to say about priests (and scribes, the religious lawyers of the day) and what they were doing:
“Tell me,” replied Jesus, “why do you break God’s commandment through your tradition? For God said, ‘Honour your father and your mother’, and ‘He who curses father or mother, let him be put to death’. But you say that if a man tells his parents, ‘Whatever use I might have been to you is now given to God’, then he owes no further duty to his parents. And so your tradition empties the commandment of God of all its meaning. You hypocrites! Isaiah describes you beautifully when he said: ‘These people draw near to me with their mouth, and honour me with their lips, but their heart is far from me. And in vain they worship me, teaching as doctrines the commandments of men’.”(Mat 15:3-9)