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.