The position of Washington on the subject of Shay's and the Whiskey Rebellion was not technically hypocritical. Washington was not against taxation nor did he support rebellions. He was against taxation without representation (and highly likely he would have supported remaining part of the Empire, with the king as head of state, as long as the colonies had either parliamentary representation or could deal with the king directly through their own colonial governments). And by the time of Shay's Rebellion, Washington was a staunch advocate of a stronger Federal union and had privately worried that a rebellion like the nature of Shay's could throw the colonies into political upheaval, which could end disastrously (either a series of bloody internal fighting or a weakling of the states and later subjugation to a European power). So put simply, Washington was not an anarchist just because he supported succession from a government in which he had no representation. He strongly supported a nation governed by laws made at the behest of the people it served. Adams, Hamilton and Madison would all fall in this camp. Franklin, while I cannot say for certain, is unlikely to not share this view as well, given his support for the constitutional convention. Jefferson is more complex. His position on Shay's relative to his own actions as President likely would have been the most hypocritical (although again, I'd label it more as complex).

Source: Washington: A Life, By Ron Chernow and Hamilton, by the same author

edit: I should add that the idea that either the Massachusetts government (that Shay rebelled against) or the Federal government and their whiskey tax (that the Western Pennsylvanians rebelled against) were tyrannical is very subjective, and your question is based on that foundation. I am very sure that the men running those governments and most of their contemporaries would hardly consider them tyrannical. And their actions towards the rebels afterwards, would be a good example of why they should not actually be considered tyrannical (most were not punished).

I'm going to focus specifically on Jefferson's response to Shays because we do have such a direct (although politically muddy) answer.

Jefferson has a famous "tree of liberty" quote that actually comes in reference to Shays Rebellion. He was in France at the time and included it in a letter to a William Smith.

The tree of liberty must be refreshed from time to time with the blood of patriots & tyrants.

This seems pretty clear, but we really have to look at the context to make sense of it. Leading up to the quote, he writes:

We have had 13 states independent 11 years. There has been one rebellion. That comes to one rebellion in a century & a half for each state. What country before ever existed a century & a half without a rebellion?

He's trying to downplay the significance of the insurrection. This is because Shays was seen as a rallying cry for a stronger national government and the to-come Constitution.

Jefferson (before his own "revolution" of 1800) is concerned about the momentum the Federalists have in pushing forward these changes. The entrenched elites were concerned about the strength of the state governments in being able to quell these types of rebellions. The possibly result is a federal state that he doesn't want to get too strong.

Some would say Shays almost got out of hand though. After his own militia failed to act (because the militia members were largely neighbors, friends, or part of the Shaysites themselves), Governor Bowdoin requested his neighboring states to help by using their militias, but he received no such assistance. So, lacking a federal army to ask (remember, we're still in the Articles of Confederation here), Bowdoin has to use the Bostonian merchant's deep pockets to cull together a last-minute force of mercenaries. More info in a previous comment of mine.

Jefferson clearly believes that the rebellion could have been controlled differently. He writes that it was created largely out of "ignorance, not wickedness", and later includes:

The remedy is to set them right as to facts, pardon & pacify them.

Jefferson either earnestly didn't think the rebellion was a big deal, or he just said it wasn't a big deal in order to mitigate the political capital the event created for the Federalists. (I'm genuinely curious; did he know the Shaysites tried to raid the federal arsenal in Springfield?)

Best books for Shays readings are Szatmary's Shays' Rebellion: The Making of an Agrarian Insurrection and Leo Richards's Shays's Rebellion: The American Revolution's Final Battle.

One other note that might be of interest is that the greatest clarity of all in this though comes from Samuel Adams, who saw no contradiction between supporting the American Revolutionary efforts and denouncing the Shaysites. He was aghast at the notion of Shays and Co. rebelling against a republic. It seemed inherently contradictory to him to be part of the government as a citizen, but then try to topple it:

In monarchies the crime of treason and rebellion may admit of being pardoned or lightly punished, but the man who dares rebel against the laws of a republic ought to suffer death.

It's probably worth nothing that as a Bostonian elite, he was exactly the kind of person that the Massachusetts farmers in debt would have labelled as a tyrant.

Oh, how the tables so quickly turn.

The idea that the founding fathers intended individual citizens to overthrow the government some day, and that that was the intent of the 2nd amendment, is profoundly ahistorical, and a very recent invention at that.

In Akhil Amarr's America's Constitution: A Biography and other writings where he traces the evolution of the texts through the founders' personal letters and through the documents they quoted, he establishes (to my mind, beyond all shadow of a doubt) that the 2nd amendment was a political compromise between northern voters, who wanted state militias to be politically independent of Washington in case things went bad, and southern voters, who wanted to make sure that all white men were armed, not as a precaution against the federal government, but as a precaution against slave uprisings.

The rebellions you cite fail on both grounds, in that it wasn't state legislatures or state governors who authorized the rebellion and it wasn't in defense against a slave rebellion.

And frankly, the whole idea that the US would tolerate armed rebellion got pretty thoroughly eradicated in 1865. Amarr turned up writings on both sides of the issue of whether or not the Constitution was intended to make political union permanent and inescapable, it was an issue that got kicked down the road, like the ultimate meaning of the 2nd amendment. And now it's pretty well settled.

So related question, i was under the impression that jefferson specifically and the founding fathers in general really backtracked on these ideas when they saw the reaction to the french terror. Is this true?