In "Self-Reliance," Emerson has no kind words regarding society. He essentially sees society as the bane of the individual, poisonous to every person's potential to grow into a unique person:
Society everywhere is in conspiracy against the manhood of every one of its members. Society is a joint-stock company, in which the members agree, for the better securing of his bread to each shareholder, to surrender the liberty and culture of the eater. The virtue in most request is conformity. Self-reliance is its aversion.
The term "joint-stock company" literally refers to companies whose stock is wholly owned by the shareholders. By comparing society to such an entity, Emerson is claiming that people who dedicate themselves to pleasing society essentially surrender all their liberty to it. They become owned by society rather being fully themselves.
Emerson argues that most people are capable of thinking independently when they are alone—that is, when they are not concerned with other people's judgments. However, in a group setting, the individual often wonders what the group will think of what they have to say, and they tailor their ideas accordingly. In some scenarios, such compromise is a virtue, but Emerson is talking about people's tendency to commit themselves to values and ideas they do not themselves believe in for the sake of social conformity.
Ultimately, Emerson wants his readers to stop valuing the opinion of society, which tends to be shallow and stagnant in its thinking. He stresses the importance of the integrity of one's own mind, even at the cost of being misunderstood.