The U.S. only desegregated, legally, in the early 1970s, just over 40 years ago. Even with legal desegregation, the history of housing discrimination, the start of the war on drugs (not so subtly a war against black folks [see powder cocaine vs. crack cocaine use and arrests]), the mass incarceration of black men, and systemic bias in nearly all facets of American life (education, policing, housing, job discrimination, etc.), have seriously stunted the prospects of many black Americans, many of whom were still reeling from generations of cyclical poverty after the end of American slavery only a century before.
More recently, attention has been drawn specifically to police discrimination against black men, as the ubiquity of camera phones and police cameras have brought to light the police' use of extreme force, especially as it relates to the deaths of many innocent and almost exclusively unarmed black men in police custody (see Mike Brown, Alton Sterling, Philando Castile, Walter Scott, Eric Garner, Tamir Rice, etc.). That's what Colin Kaepernick began protesting by first sitting, then kneeling during the playing of the national anthem before NFL games, and that is what Trump is reacting against.
There has also been a dramatic rise in the number of avowed white supremacists, many of whom voted for Trump based on his rhetoric of fear (many white Americans are fearful that they are losing out to minorities as the battle for racial equality becomes more real), and the proliferation of these supremacists concurrent with Trump's presidency (not a coincidence) has left them empowered to organize in a way that bigots have not felt comfortable doing since desegregation.
This is obviously a very simplistic answer to a question which can only be answered fully with an immersive study of 300 years of racial oppression in this country, but hopefully it gives you an idea.