The term was taken from the "Fight Club" line: "You are not special. You're not a beautiful and unique snowflake." The term was applied to those who needed 'safe spaces' to protect them from hearing or seeing anything conservative, even seeing the name "Trump" chalked on a sidewalk. It is now a term for somebody who thinks they take the high road, are morally superior et al but are not. . .and is most often used as a put down for those who are easily offended or need a 'safe space' or want the government to impose the snowflakes' values or wants on everybody. And they feel perfectly justified in violating anybody's rights who disagree with them.
The term predates Fight Club for starters, this has already been established so catch up.
However Fight Club makes no political inference in it's use of the term, it's all in the eye of the beholder. So, I can call jc456 a snowflake because he's afraid of black people and he has to cover that up by pretending to be a tough guy on the internet.