The SeaBus connects the downtown core of Vancouver to a dense suburb along a route which is significantly shorter than the best road connection.
This is also why the Dartmouth Ferries work in Halifax, why the Thames ferries work in London, why the river ferries work in Manhattan, etc. These routes cross bodies of water in ways that significantly shorten the journey geographically.
In Toronto, the only commute distance where you really get this advantage is between Ookwemin Minising and downtown. The Islands aren't a commuter destination, and any other route would take you laterally along the shortline, rather than across a body of water. (Meaning you aren't saving any geographic distance, and the ferry therefore ends up being slower and more expensive than a land-based service.)