Yeah, why are people taking taxis back? Strange.
Actually, it's not strange at all. The ferry trip from Manly to Sydney's Circular Quay is about the same distance as taking Sdyney Road west, Spit Road south and west and Waringham Road south across the famous Sydney Harbour Bridge.
In addition to that consider these facts:
1. it takes time to get to Manly ferry terminus from Shelly Beach; (indeed, it would for either option, as according to my map Shelly Beach is many kilometers north of Manly)
2. with taxi you go direct with no delays
3. ferries operate either once per hour (FAST ferry) or at 15 and 45 after every weekday hour such as 11215pm and 1245pm (regular ferry)