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 be great is to be misunderstood.

This quote means that it is not necessarily a bad thing to be misunderstood. Examples are given of famous figures in history who were misunderstood. These figures were great, so their greatness was the result of being misunderstood. In other words, people who do great things, but are not always understood, are likely to be remembered for their achievements.