While many modern environmentalists paint Thoreau as an anti-government libertarian free spirit, it must be pointed out that the American government of his day was very limited in its powers. It also openly espoused individual liberty and Manifest Destiny. In other words, to be a rebel against the limited constitutional powers of the American government suggests that Thoreau was not the libertarian or free individualist that many often make him out to be. He was protesting/rebelling against a limited government based on liberty and Judeo-Christian values.
Slavery?
He was protesting against the expansion of slavery.