This answer is based on two biographical works on Paine, one by Christopher Hitchens and the other by Bernard Vincent.

To begin with, I’d like to give the whole quote which might help to understand his reasoning:

“And as to you, Sir, treacherous in private friendship (for so you have been to me, and that in the day of danger) and a hypocrite in public life, the world will be puzzled to decide whether you are an apostate or an impostor, whether you have abandoned good principles, or whether you ever had any.”

He also accused Washington of political duplicity and military incompetence. I can’t say how much of the accusations held up to the facts, but a good part of the reason why Paine would publicly say such things is the feeling of betrayal he had for Washington, puzzling considering that just five years before, in 1791, Paine had dedicated the first part of the Rights of Men to Washington “one of the most conservative revolutionaries of all time”(Hitchens, p. 17), “a small Treatise in defense of those Principles of Freedom which your exemplary Virtue hath eminently contributed to establish”.

We can only understand this feeling by looking at Thomas Paine’s biography. Born in England, where he began his political writing, Paine went to America by suggestion and with recommendation from Benjamin Franklin in 1774. I won’t go into detail on his contribution to the American Revolution, where he even served as an aid-de-camp to Nathanial Greene, but the influence of his pamphlet Common Sense (1776), a bestseller by any standards with at least 500.000 people having actually read the pamphlet, on the public of the time can’t be underestimated, on par with that of Washington and Franklin (Vincent, p. 11). He continued being directly involved in American politics and in 1781, Paine was a member of de delegation sent to Paris to solicit the aid of the French King in the war, which would be instrumental in the capitulation of the British.

Hitchens tells us that in America “Paine had urged the wealthy to contribute their share for defense, and had set an example by foregoing royalties on his pamphlets”, which gained him some enemies in the traditional elite, among whom Hitchens cite Governeur Morris. Washington, on the other hand, had urged a public vote of money to Paine, which didn’t go through, but in the end, he did receive a property from the state of New York.

Back in Europe in 1787, Paine saw the beginning of the French Revolution and envisioned and England equally free. He got into a heated argument with Edmund Burke on the right of tradition and the rights of men of new generations in making their own institutions. The Rights of Men is his answer to Burke and for that he was banished from England in 1792 for treason. However, before the sentence was passed and even before he had set mind to flee his country, he had already been made a French citizen and elected deputy of the Convention in four different departments.

Paine flee to France and got directly involved in the French Government and when the trial of Louis XVI came, he argued that the King shouldn’t be decapitated, for the danger was in the institution of the monarchy and not in the individual itself. He was also concerned that for Louis’ role on the American Revolution, his death might offend the only firm ally France still had, the Americans. What followed, of course, was the decapitation of the King and then the Terror, when Paine was imprisoned as an Englishmen, even though he was recently banned and no longer a subject of His Majesty.

Paine remained in prison for nearly a year and was one of the few to escape with their lives. This was either by chance, by having the cross indicating that he was to be executed drawn on the wrong side of his cell door, or his death might have been deliberately delayed by Robespierre as suggested by Bernard Vincent. Through this whole time of danger, though, the American ambassador in Paris was Gouverneur Morris and not him nor Washington ever made serious pressure on the French Government to free Paine. When James Monroe, the new American Minister in Paris, arrived, Vincent says he obtained Paine’s liberation “by simply claiming him ‘as an American’” (Vincent, p. 89). What Vincent also states is that with the dampening of French-American relations by the Terror, Washington and Morris had been turning increasingly towards England, which Paine saw as betrayal of the alliance forged with the French during the Revolutionary War. Uncompromising and radical as he was, this double betrayal must have been unthinkable to Paine and he would never forgive it.

Bernard Vincent. The Transatlantic Republican, Thomas Paine and the Age of Revolutions. 2005 Chistopher Hitchens. Thomas Paine's Rights of Man: A Biography. 2008