Jefferson was NOT advocating rebellion in this quote. Not even close.
From the letter (he is speaking of Shay's Rebellion):
Jefferson was saying that rebellions are not a sign of weakness for a healthy democracy, and that the threat of them keeps the government honest. He was certainly not saying they should actually succeed, nor did he think we needed a new constitution every few generations.I say nothing of it's motives. They were founded in ignorance, not wickedness. God forbid we should ever be 20 years without such a rebellion. The people cannot be all, & always well informed. The part which is wrong will be discontented in proportion to the importance of the facts they misconceive. If they remain quiet under such misconceptions it is a lethargy, the forerunner of death to the public liberty. 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? & what country can preserve it's liberties if their rulers are not warned from time to time that their people preserve the spirit of resistance? Let them take arms. The remedy is to set them right as to facts, pardon & pacify them.
Note that he wrote that the rebels were ignorant.