Emerson is commenting on how many great men followed their own intuition in spite of criticism or misunderstanding from society. He says,
"Is it so bad, then, to be misunderstood? Pythagoras was misunderstood, and Socrates, and Jesus, and Luther, and Copernicus, and Galileo, and Newton, and every pure and wise spirit that ever took flesh." To that he adds "To be great is to be misunderstood."
In context, Emerson also says that great men are not always consistent. In fact, "A foolish consistency is the hobgoblin of little minds, adored by little statesmen and philosophers and divines". Thus, if one is not always consistent, one may be misunderstood. But, since many great men have not be understood by society, then you are you have great company when people don't understand you. What is important, according to Emerson, is that one not violate his or her own nature. You must be true to yourself, even if it mean saying one thing one day and saying something else the next day. That way we show that we trust ourselves and not others to dictate our beliefs.