Thomas Jefferson was a strong believer in individual liberties, personal freedoms and a weak government, essentially he believed that no government should be able to have some sort of ultimate authority over its people, but rather that the people should always have the power to change government and policy. Shay's rebellion took place because the federal government was taxing its citizens, the southern farmers however didn't have the actual physical money to pay their taxes, however they did not refuse to pay, they stated that they could pay their taxes in crops, because that is what they had- which actually wasn't that far fetched for the time period. The government said no, they would not accept crops for taxes. As a result a rebellion started. Jefferson basically meant that a rebellion is the people's way of saying that the goverment may be doing something wrong, and that it is important for the people to stand for what they believe in, even if it causes the government a headache, again remember that he believed in a small federal government and individual freedom above the rights of the nation- so he would've seen a rebellion as an opportunity for the government to examine its own practices to make sure they're governing justly and that they aren't in the wrong or if they are- to seize the moment and fix it for the sake of the citizens.