Simplify Cap Metro fare system, offering 3 hour (trip), 24 hour, 2 day, 5 day, and monthly passes.
Avoid charging per connection: a trip on the bus system will cost you the same amount, no matter where you go or how long it takes you to get there. Longer distance commuters are currently discouraged from mass transit if they are not on one of the more major lines.
Simple = beautiful, in this case. I would say $2 for 3 hour, $5 for day, $30 per month would be reasonable rates to encourage people to use the system.