In Ye Olde Dayes it referred to someone who had control or authority over a place, object, craft, etc -- a teacher would be a master for example. It's a common word across European languages, and certainly predated the atlantic slave trade.

Probably descended from the Latin word "magister", which (despite Rome having plenty of slaves) didn't neccersarilly refer to a slaveowner -- indeed many Roman slaves were Ludi Magister -- educated slaves that were teachers at Roman schools

Etymology of "master bedroom" seems to come from "Master's bedroom" in boarding schools, where it was the bedroom that the school master occupied (with Master having descended from Roman times)