Spectators chanted abuse as Johnson paraded in front of the main stand after the race, which he won in 20.29sec, comfortably beating his fellow American Jon Drummond.
Johnson's popularity took a huge dip in Brazil after media reports alleged he had pushed away a young fan who had wanted to pose with him for a photograph at his Copacabana hotel.
Johnson, who wore purple running shoes instead of the gold pair he used at the Olympics, shrugged off the controversy.
"I came here to run my race. I've run it and now I'm going home," he said. "That's my job. I'm not here to worry about the crowd. I've never had any problem like this before."