First of all, the information available does not lead to your conclusion that Jefferson is "not sceptical, and he is enlightened."
In your incompletely quoted sentence, the pair of linked adjectives 'skeptical but enlightened' work together to describe the noun 'intellectual' -- the meaning would be that 'the intellectual in question is skeptical; however (he) is enlightened' as in 'being skeptical doesn't prevent (this intellectual) from being enlightened', to expand the meaning.
The word 'but' as used here is unrelated to 'far from' as used at the beginning of the sentence.
Since the second half of the sentence is not quoted, quite a little context is missing, but 'far from' is usually used to mean 'does not do', 'does not mean to' 'does not intend to' or 'disagree' as in 'it is not (my) intention to view Jefferson as a skeptical but enlightened individual...' or 'I disagree with the way some people view Jefferson as a skeptical but enlightened individual...' as pointed out by the learned members in comments.
Moreover, 'far from' implies the meaning 'not that, but quite the opposite' where there is no need to explicitly state 'but', since it is usually implicit in 'far from'.
Far from praising the student's efforts, the teacher strongly criticised his lazy work.
Far from holding him up as a fine, upstanding citizen, I consider him an unmitigated scoundrel.
Note: but is used in the same sentence as far from only to suggest some mitigation, and only in a more complex construction such as
far from praising his efforts, the teacher criticised his lazy work, but agreed that his basic argument was valid.
Note 2: As the member has mentioned in comments,'far from' is also used in the sense 'not at all', 'insufficiently' or 'not really' as in "they were far from pleased with his sneaky trick", "his explanation was far from satisfactory" or "his answer was very far from the truth."