In "Civil Disobedience," Thoreau asserts the right of an individual to follow his or her conscience to do what he or she feels is right, even though the state may not agree with him or her. In this paragraph, he supports his assertion by referring to abolitionism, the campaign to end slavery. He believes that abolitionists should not support the state, either by fighting in the army or by paying taxes. He also states that abolitionists should not wait until they are in the majority because they are in the right morally to protest slavery. Instead, if someone follows his or her conscience and believes that slavery is wrong, that person already constitutes a majority, meaning that person already has the right to protest the government's actions and refuse to fight in the army or pay taxes. If one is morally right, he argues, that person does not need to wait until others agree with him or her before acting. 

Referencing what he called "the machine of government," Henry David Thoreau, in his treatise On the Duty of Civil Disobedience, declared that it was a moral and practical imperative for the individual to confront the wrongs committed by the state.  Thoreau was exceedingly skeptical of government and of its institutions, and believed fervently that it is the responsibility of the individual to take it upon himself to resist policies and practices that run counter to the government's own assertions of good intentions.  As he wrote in his essay, "If it is of such a nature that it requires you to be the agent of injustice to another, then, I say, break the law."  As Thoreau continues to discuss the moral imperatives of civil disobedience, he reaffirms the importance of the individual in addressing the wrongs that arise from misguided policies.  It is in this vein that he wrote the following:

"I do not hesitate to say, that those who call themselves abolitionists should at once effectually withdraw their support, both in person and property, from the government of Massachusetts, and not wait till they constitute a majority of one, before they suffer the right to prevail through them. I think that it is enough if they have God on their side, without waiting for that other one. Moreover, any man more right than his neighbors, constitutes a majority of one already."

Thoreau is, again, emphasizing the need to resist unjust policies and practices, including those policies codified in law.  Just as the Founders asserted in drafting the Constitution, the imperative of preventing a tyranny of the majority over the minority was as important to a democratic form of government as the need to prevent a tyranny of the minority over the majority.  The numbers, in other words, are less important than the morality. A "majority of one," then, refers to the inordinate influence that can be brought to bear against unjust laws by the single individual determined to resist those laws' application.

In this statement by Thoreau, he is saying that the one person who is on the right side of the question counts for more than all the people who are on the wrong side of the question or issue.  If you are correct in your belief, your belief would be more important and be a majority of one over whatever number of people are against you or on the other side of the issue.  Thoreau believed that personal beliefs rightly held were more important than any government rule, and thus he promoted civil disobedience against any rule which he considered wrong.  As a writer, Thoreau was a powerful voice for following an individual's own conscience and beliefs no matter what the government wanted the public to believe.