The answer can be found in one of his quotes: "I prefer dangerous freedom over peaceful slavery" (this can also be translated to: I prefer the tumult of liberty to the quiet of servitude).
This last sentence is closely linked to this: "I hold it that a little rebellion now and then is a good thing".
Jefferson, in these two sentences, demonstrates that the most dangerous thing that a rebellion, is the consequence of not rebelling, in times in which the governments are authoritarian. The rebellion here, is held by Jefferson as something of extreme necessity, for the maintenance of social equilibrium, when it comes to social balance, economic, government and legislation.