In Ralph Waldo Emerson's "Self-Reliance," the main idea is that the individual should exist apart from society. In other words, people should be themselves completely and not seek to conform to social norms.

The quotation "Society everywhere is in conspiracy against the manhood of every one of its members" is a strong statement. The way Emerson describes society here makes it into an antagonist that is actively working against individuals. Society "conspires" to get individuals to conform to its expectations. When he says "manhood," Emerson seems to mean individuality, but the connotation is also that society emasculates individuals when it asks them to conform. This implies that individuals are weaker when they aspire to be liked or approved of by others; they are stronger when they behave according to their instincts. In a similar quote, Emerson claims, "For nonconformity the world whips you with its displeasure." The verb "whips" connotes the violent reaction of society against nonconformists and indicates that those who dare to be themselves risk punishment from the community. 

Elsewhere in "Self-Reliance," Emerson furthers the idea by saying that the individual not only should not concern himself with loyalty to social norms, but he also has no obligation to conform to any idea of consistency in his own being. In a famous passage, Emerson asks, "Do I contradict myself? Very well, then I contradict myself. I am large, I contain multitudes." He indicates here that to be an individual is to be complex. There is no need to be "consistent" to some false idea of who one is, just as it is foolish and unnecessary to mold oneself to a social ideal. 

For Transcendentalists such as Ralph Waldo Emerson, individualism is paramount. Railing against imitation, Emerson encourages people to become self-reliant and listen to their inner thoughts. They must avoid "the opium of custom" and behave according to their own thoughts because "society everywhere is in conspiracy against the manhood of everyone of its members." In other words, people must not be lulled into following customs and letting others think for them or make rules for them. Society, Emerson says, is a "joint-stock company" that agrees upon ideas for one goal. However, in so doing, individuals surrender their individual liberties. And, once these liberties are surrendered, it is very difficult to gain them again because people will still want to control someone over whom they have already control. And, for Emerson, the most important thing is the "integrity of one's mind." 

Always, then, an individual must be one's own person, thinking one's own thoughts and possessing one's own principles. Perhaps, one will be misunderstood, but men such as Luther, Copernicus, and Galileo have been misunderstood, as well, observes Emerson. For, "to be great is to be understood," Emerson adds.

Ralph Waldo Emerson was perhaps the foremost of the American Transcendentalists and it is the philosophy of the Transcendentalist movement that is reflected in the passage you quote.

To the Transcendentalists, "manhood" (in today's language, we should probably see "being fully human," perhaps) is evidenced by doing your own thing, following the dictates of your own conscience.

By contrast, Emerson argues, society conspires to rob us of our "manhood" by making us conformists.   In the very next paragraph after the one you quote, Emerson writes the famous line "whoso would be a man must be a nonconformist."  To him, society tries to prevent us from being "men" by forcing us to conform.