Reading that Jefferson purportedly said "question everything" I just had to question if he actually said that. I'm no student of Jefferson, but I find it difficult to believe he was such a relativist that there were no things known that were absolute. But I could be wrong.
Looking up  "Thomas Jefferson" and "question everything" I did not find this quote: In a eulogy to Franklin, he referred to lawyers as people “whose trade it is to question everything, yield nothing, and talk by the hour".  (As is common, the Founding Fathers are often misquoted in a way that supports mostly right wing Tea Party ideology )
I did find this quote: "Question with boldness even the existence of a god; because, if there be one, he must more approve the homage of reason, than that of blindfolded fear." So the irony is that if we are to ascribe "question everything" (no exact quote) to Jefferson, he used it in reference to religion. 
"If there be [God]"? Tom was often accused of being an Atheist.