The CPR ran harbour to harbour before BC Ferries came along, but these smaller boats that are trying to make a go of it are not feasible in the lumpy gravy weather during the winter.
The crossing is too long and there ain't too much to do, so most folks would rather travel on a ship with more amenities.
It was also an era when harbour to harbour flying was not available.
CP and Union Steamship provided a lot of services up and down the coast till the late 50s because it was the only way to get a lot of places. With more roads and more cars, the nature of ferry travel changed.