Thomas Jefferson is the president who worked most for the freedom of individuals. Some will mention that he had slaves, but this is a non-issue, honestly. It's like saying a company is bad because they used a cancer-causing insulation decades ago. It was common practice. Doesn't make it right, but it absolves him from being singled out.
Jefferson was a federalist in the real meaning of the word, not the meaning employed by The Federalist and other such writings and modes of thought. Those ideals, championed by Washington, Adams, Alexander Hamilton, and more were not federalist in any way. They were nationalists, wanted to create an all-encompassing national government to be in charge of the states. A real federalist, like Jefferson, pleaded for a limited federal government with no real control over the individual citizens of each state. It would act as an instrument of organization between the sovereign states. The state governments would be independent and in charge of leveeing taxes and enforcement of their own laws.
Funny thing: the feredalist ideal won in the ratification debates, as we can see in our Constitution's final draft. This is also why we have the FEDERAL GOVERNMENT and call this land the UNITED STATES OF AMERICA. However, due to brazen disregard for the limited powers given the federal government, Washington, Adams, and many more Presidents who are called "great" used their positions, by executive order and by alliances within the Congress and Supreme Court, to distort the meaning of our Constitution within decades of its ratification.
Jefferson is one of the few Presidents who could claim that he fought for the rights of free men, and not be lying.