Why does Thoreau believe that "a government in which the majority rule in all cases cannot be based on justice, even as far as men understand it?"

This quote comes in the 4th paragraph of “Civil Disobedience:”

After all, 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. Can there not be a government in which majorities do not virtually decide right and wrong, but conscience?

Thoreau makes a solid point that our rules and laws are often made, not with common sense as the guideline, but solely by the number of people who agree. The assumption is that the more people we can count who believe in a certain stand on an issue, the more right and correct this stand is. And Thoreau wrote this essay well before legislators got the sizable contributions they get today from lobbyists, corporations, and special interest groups. Now he would have to add to the mix the number of dollars spent promoting an issue as well. He maintains that “majority rule” ignores the rights of the individual who may have good reason to act on his own belief system, his own higher law:

Must the citizen ever for a moment, or in the least degree, resign his conscience to the legislator? Why has every man a conscience, then? I think that we should be men first, and subjects afterward. … The only obligation which I have a right to assume is to do at any time what I think right.

Think of any controversial issue we have today, and you can apply Thoreau’s interpretation to it. The use of medical marijuana and the right to have an abortion both come to mind. These are actions that may make perfect sense in specific individual situations, but which other people may oppose no matter what, and over which laws have come into question. Thoreau thinks government should be set up to allow for such individual differences to thrive, and somehow without breaking the law.