There are several regular bus/shuttle services on the main highway from Dunedin to Queenstown (via Roxburgh) through Clyde, while some others follow the actual Rail Trail route.
Some Trail Operators (Bike hire, etc.) have their own coaches and will pick up or drop off their customers and bikes at different places and also arrange for luggage to be transferred to the next accommodation.
A public bus service follows the Ranfurly route and also passes through townships along the way.
Many accommodation hosts will go out of their way to pick you up, and arrange for your luggage to be forwarded to your next stopover.