The term is supposedly racist. Ironically, the article itself reveals that the term originated long after the end of slavery:
“The first thing we did was Google the phrase and expect to find some dark history of why it was called ‘master bedroom,’” said Mr. Conlon. “But no, it’s a marketing term.”
The first recorded usage of “master bedroom” seems to have been in a 1926 Modern Homes catalog by Sears, Roebuck and Co. The pamphlet offered potential buyers a kit they could use to build their own homes.