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Where I live (sub 30k city, but decently dense in the parts people actually live in), the problems are:
1. Frequency. Fixed routes run every 45 minutes from 6 am until 6 pm, then every 90 until the last bus at 10. This sucks and can't be changed unless more people ride the bus (around 2k daily riders, but apparently only around 1% of people in the city use it to commute to work, which makes me think a lot of the riders are elderly or disabled).
2. Destinations. A lot of the places people want to go are located on roads that are actively hostile to pedestrians (a lot are also literally highways). It's easier to just get a car than pray drivers actually obey traffic laws. Downtown is safer for pedestrians, but a lot of it was bulldozed for either parking, or ugly concrete globohomo buildings, so there's not much to do there. The construction of a mall in the 80s also took a lot of stores away (including one the city did a lot of the bulldozing to support). Residential neighborhoods have some businesses, but they're few and far between.
3. Perception of safety. People think this is New York or Seattle, and that if they set foot on the bus they'll immediately be mugged or have to sit near an unpredictable schizo/junky.
more minor reasons:
4. There's almost no marked bus stops. Sometimes there's a sign, or a bus shelter, but most of the time you have to flag the buses down on random streets.
5. Their website sucks. The time estimates only give the start and midpoint of a route, and there's no indication in what direction the bus travels. This has gotten better with the transit app and bus tracking.
