When answering this question, it's important to understand the concept of government as held by Jefferson and set out in the Declaration of Independence. Jefferson believed that governments exist to secure what the Declaration calls “certain unalienable Rights,” such as “Life, Liberty, and the pursuit of Happiness.”
If, for whatever reason, any form of government is unable to secure these rights, in other words, to do what it is expressly established to do, then the people have the right to alter or abolish it and institute a new form of government.
Jefferson's notion of government is quite radical for its time. The prevailing opinion in Europe at that time held that existing institutions of government could only be subject to gradual, piecemeal change over time. Anything more radical than this would invariably lead to chaos, disorder, and instability. The idea that governments existed to secure certain abstract rights, and that if they didn't secure them they could be abolished, was a dangerous notion to most Europeans at that time.
To be sure, Jefferson states quite clearly that the decision to abolish an existing form of government should not be taken lightly. It's only after the people have suffered “a long train of abuses and usurpations,” such as those inflicted on the American people by King George III, that it becomes the right and duty of the people to get rid of the government and start over.