The rebellion Jefferson refers to is Shay’s Rebellion, which took place in western Massachusetts in 1786 and 1787. According to Wikipedia “the Shaysites' grievances extended beyond the specifics of Massachusetts' economic situation to issues like: rule by a faraway elite; cronyism and corruption in government; and regressive tax policy.”
The same evils prevail today, but in light of the government’s vastly superior resources in weaponry and surveillance, and despite the strenuous efforts of the NRA, the kind of armed rebellion that Jefferson called for in his letter to Smith is no longer feasible.
Fortunately, a satisfactory substitute for a popular uprising now presents itself in the guise of a Trump vs. Sanders Presidential Election. The constitutional crisis that will ensue after either of these gentleman becomes executive and commander-in-chief – as the Washington establishment tries to deal with either a petulant bully for whom nuclear war would be a minor inconvenience compared to having his ego thwarted in any way, or a Leveller in whom are combined the European Proudhonism of the Brooklyn Bund and the American self-righteousness of the New England puritan, and who regards any capitalist whose social conscience does not meet the standard set by Ben and Jerry as an enemy of the state – will provide the political purgative to return our country to the simple beatitudes of the Declaration of Independence (which plays the same role in our vast accumulation of laws and policy papers which the Sermon on the Mount plays in the New Testament).
No fear – the blood which, according to Jefferson, is required to refresh the tree of liberty will be shed, most likely not during the post-election upheavals, but before – during the Presidential campaign – when those Americans whose moral standards are so high that they have refrained from using their share of the country’s 324,849,820 guns for such private gratification as avenging the humiliation of being cut off on their way to the E-Zpass lane or teaching a lesson to a cranky spouse, at last will be able to employ them in upholding eternal principles handed down by whichever television network has won their allegiance.