Back in the 1960s, I couldn’t always keep track of what people were talking about, between the Vietnam War and Black Power.
“Charlie” seems to have been military slang for the Viet Cong. (And then there were usages like “Charlie Company” and “Checkpoint Charlie,” which were just a way of vocalizing the letter C.)
“Mister Charlie” seems to have been ghetto slang for “The Man” or something like that.
Ever wonder how the same nickname happened to be applied to such different phenomena?
As for the Viet Cong, the name “Charlie” came about as an abbreviation for “Victor Charlie,” i.e. a military vocalization of “V.C.” (Remember the old “Able Baker Charlie” code? That goes back to radio communications, where they had to spell out each letter of the alphabet with a whole word to make for unambiguous transmission.) My memory of being a kid in the 60s is a little hazy now, but I think when we played war games we mistook “Charlie” to mean any kind of Oriental enemy of Uncle Sam, including the Japanese. Then there was an epsiode of The Time Tunnel circa 1967 where they go back to Iwo Jima and a Japanese soldier captures one of the time travelers and calls him “Joe.” He says, “I call all 'Mellikans Joe 'cause they all rook same to me.” That only confused my kid brain further!
On the home front, James Baldwin wrote a play called Blues for Mister Charlie (but I haven’t read it; what’s it about? ). And the Grateful Dead did a hoodoo song, sung by Pig Pen: “Mister Charlie tole me so.”