The color indicates whether the majority of people in each county voted for Republican Candidate - Donald Trump (Red) or Democratic Candidate - Hillary Clinton (Blue).

I have downloaded the data from a Github repository called "County_Level_Election_Results_12-16" maintained by Tony McGovern (https://twitter.com/tonmcg). The 2016 data there was originally scraped out of Townhall.com's 2016 election result page.