What problem does thoreau see with majority rule?

In his essay, "Civil Disobedience", Thoreau states that majority rule is not based on "justice nor fairness" and that it is only based on the strength of the majority over the minority. In a political and socioeconomic system that denies the moral conscience and compels individuals to do wrong or be wronged by others, Thoreau's widely apparent deontological stance on philosophy is in direct conflict.

What matters is who is right, the majority rule is not based on right and wrong, based on individual conscience decide right and wrong, have to figure out what you really think.