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Mainly because the city is so sprawling Alison. Everytime I go to Brisbane or Sydney I come home thinking there should be far greater use of the river to ease traffic congestion.
Unfortunately we are very car orientated community without a solid corridor structure to our transport networks. Remember for many years we only had three train lines (Freo, Midland, Armadale) and the freeway was only about 10kms north and south.
I do agree that they should have a ferry system though, Guildford to Perth, up to Canning or Shelley even, Melville foreshore and obviously up from Freo. Maybe even along the coast...