According to the Declaration of Independence, "all men" possess certain "unalienable rights" (life, liberty, the pursuit of happiness). The job of the government is to help each citizen realize these rights. Should the government act in ways that restrict these rights, the people have the right to "alter or abolish" the government.
Jefferson was writing about the colonial government of the King, of course, and his argument serves as a justification for the Revolutionary War. He includes a discussion about the need to use "prudence" in making the decision to change governments and argues that history shows that people would rather suffer than change the governmental "forms" under which they suffer. In the present case, however, Great Britain has "evince[d] a design" to place the colonies "under absolute Despotism."
Jefferson's words here have had repercussions far beyond the question of Independence. They became a basis for the succession of the Southern states, the Civil War, and the reforms Roosevelt put in place during the New Deal. They continue to shape political discourse to this day.