Both Thoreau and Emerson believed strongly in the rights of the individual.  In "Civil Disobedience," Thoreau wrote,

I please myself with imagining a State at last which can afford to be just to all men, and to treat the individual with respect as a neighbor. ["State" is metaphoric for civil government; "neighbor" is metaphoric for respect for men]

Thoreau objected to a government that dictated, for "It can have no pure right over my person and property but what I concede to it," he said.  Thoreau felt that each person's responsibility is to follow the highest leadings of personal conscience.  If these leadings are counter to civil law, then the individual must answer the higher moral law.  Thus, the contrast is between an unjust civil law and personal conscience and awareness of a higher moral law.

For Emerson, too, there was at times a conflict between society and the individual.  Thus, the contrast in "Self-Reliance" is between the individual who should "trust thyself," arriving at knowledge and moral rectitude and the society that dictates rules. (conformity vs. nonconformity)  Emerson argued that each individual possesses the intuition to arrive at sound moral judgments, an intuition that he/she should trust against public disapproval:

A foolish consistency is the hobgoblin of little minds [here is metaphoric language], adored by little statesmen and philosophers and divines.  With consistency a great soul has simply nothing to do....Speak what you think now in hard words, and tomorrow speak what tomorrow thinks in hard words again though it contradict everything you said today--'Ah so you shall be sure to be misunderstood'--Is it so bad then to be misunderstood?  Pythagoras was miunderstood, and Socrates, And Jesus, and Luther, and Copernicus, and Galileo....