Thoreau argues in "Civil Disobedience" that men who choose to act according to their consciences are treated like enemies of the state. What does this mean? Do you think that this is still true in today's society? Why?

In his opening lines of "Civil Disobedience," Thoreau states that he believes that "government is best which governs least" (Thoreau). Thoreau firmly believes that the government should not be involved in and should not dictate his daily affairs, and that if he does not agree with the government he is within his full right to protest against it. Thoreau believes that one of the ways to disobey the government is to refuse to pay taxes that go toward financing government actions that he disagrees with. During Thoreau's lifetime, he was vehemently against two big issues that his government endorsed: slavery and the Mexican-American War. Many citizens of Massachusetts (Thoreau's home state) also opposed these government activities, however, they continued to pay taxes to the federal government. Thoreau refused to pay his taxes because he did not want his financial support to go to a government that he did not agree with, and consequently he was thrown in jail. Thoreau therefore declares that "under a government which imprisons any unjustly, the true place for a just man is also a prison" (Thoreau). Thoreau followed his own conscience, but was thrown in jail because of it. He therefore believes that if one follows his own conscience it will often oppose the official government stance and that person will therefore be treated as an enemy of the state.
The second part of this question is dependent on personal thoughts and feelings, but this is comparable to the way that protesters are treated here in the US. Although we have the right to peacefully protest here in the United States, many protesters do end up spending some time in jail or having water cannons, rubber bullets, or tear gas used on them in order to help police control a crowd. Recent examples might include incidents like the Standing Rock protests of 2016.
http://www.gutenberg.org/files/71/71-h/71-h.htm