Sadly, the Outer Cape Bike Shuttle has been discontinued. According to planning staff at the Cape Cod Commission, the shuttle was only funded as a 3-year experiment. It was a dedicated bus with a trailer that could take 12 bikes (and their riders) from Provincetown to the Wellfleet trailhead of the Cape Cod Rail Trail. Funding ran out at the end of 2015, so the shuttle is no more.
Good news, though, is that all of the Cape Cod Regional Transit Authority (CCRTA) buses are equipped with a 2-bike carrier on the front, so you can still get your bike to the Rail Trail in Wellfleet without riding all the way on Route 6.
You can flag down a CCRTA bus anywhere or pick it up at designated bus stops around town at MacMillan Pier, Stop & Shop on Shank Painter Rd., the Provincetown Inn, and the East End Playground at Howland St.
The "FLEX Bus" runs year-round and meanders through the Cape towns for a scenic but very long ride all the way to Harwich (it takes 2 1/2 hours to go all the way from one end to the other).
The seasonal "Provincetown/Truro Shuttle" goes between MacMillan Pier and North Truro destinations. This service also offers a loop through the Seashore and can take you (and your bike) to Herring Cove, Race Point, the airport, the Visitor Center, and Beech Forest. Ask the driver at the pier which direction they're headed, as it's not always clear.