Thoreau feels that majority rule is incompatible with the rule of indvidual conscience. He writes:
the practical reason why, when the power is once in the hands of the people, a majority are permitted, and for a long period continue, to rule is not because they are most likely to be in the right, nor because this seems fairest to the minority, but because they are physically the strongest. But a government in which the majority rule in all cases cannot be based on justice, even as far as men understand it.
Thoreau's thinking is similar to what John Stuart Mill would a few years later call the tyranny of democracy. Just because most people think an idea or path of action is right does not make it right.
Thoreau, who was an abolitionist, had no faith in democracy—majority rule—as a means to rid the country of slavery because he didn't think the majority of people would vote to abolish slavery until slavery had more or less died out anyway. He urged abolitionists in his home state of Massachusetts to withdraw their support of the state rather than wait until they had a majority of people on their side voting against slavery. He said that having God on their side was enough to legitimize their cause.
Thoreau put the rights of the individual over the rights of the majority, writing:
Is a democracy, such as we know it, the last improvement possible in government? Is it not possible to take a step further towards recognizing and organizing the rights of man? There will never be a really free and enlightened State until the State comes to recognize the individual as a higher and independent power, from which all its own power and authority are derived, and treats him accordingly.
Thoreau doesn't offer a practical vision for how allowing every individual to do what he pleases will allow for a coherent state to operate, but he does take a strong stand against majority rule.