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In retrospect the proposed fee increase was doomed. It seemed to pit car owners (who own cars and presumably don't use public transit) against bus riders (who in the public mind don't own cars). So on the surface it's asking car owners to pay someone else's bus fares.
But of course most bus riders have cars, and as bus routes disappear, more cars that would have been happy to stay in their driveways will be on the road clogging up streets.
A second factor also played a role: voters are more likely to approve construction (new schools, roads, rail lines) then they are ongoing maintenance (teacher's and bus drivers's salaries.