Cape Air definitely has special fares when combined with other carriers. They used to run a PVC-BOS-EWR fare with CO for less than $200 RT.
If you are flying to Logan, always check the through fares to PVC. Since you are already at Logan, you save the trouble of taking a taxi to the wharf for one of the ferries. (I have taken the ferries occasionally; I really find flying to be far more convenient).
The flight takes 20 minutes. The ferry takes two hours plus for the fastest jet-cat.
Takes about 10 minutes to drive out to PVC from town. MacMillan wharf is in the center of town. I really value the total (1.5 hours) time advantage when you are connecting at Logan -- I have commuted to and from PVC from customers all over the country during the Summer months, and the time savings by flying is significant.