The stern area has always been the place near the steering apparatus (rudder, tiller, ship's wheel, etc.), and by extension became the domain of the ship's captain and other officers. In particular, the stern was the location of the officers' quarters, and during the age of sail became the most luxurious part of the ship, with rows of windows, galleries, walkways, and fine decorations. That meant that this part was rather vulnerable, and the goal of much maneuvering in battle was to achieve the stern rake, in which a ship would pour its entire broadside into the stern.
Stern of a Severn class lifeboat (UK)