The correct answer to this open question is the following.
Jefferson differed from Hamilton in that he supported an anti-federalist government when Hamilton supported a strong central government.
We are talking about the conflict between federalist and anti-federalist of the 1790s. Their differences were over a strong federal government against strong states. Hamilton wanted to support wealthy businessmen and the creation of a National Bank. Thomas Jefferson believed that a strong federal government could end up being a dictatorship like the British monarchy and he did not want that for the United States.