Santa Cruz installs bike racks with a capacity for three bicycles on their buses. The district spends about $1000 to purchase and install each rack on a bus. Of the 27,204 passengers who rode the Highway 17 Express last November, 1745 (6%) brought their bikes on the bus.
The Highway 17 Express makes 28 trips daily from Santa Cruz into San Jose. That's potentially 84 passengers who bring their bikes on the bus. If you like visual comparisons, I've grayed out 84 parking spots (of 225 available, or 37% of the parking spots) in the image below of the Park & Ride lot in Scotts Valley.
When a commuter parks in a Park & Ride lot, that parking space is unavailable for the entire day. Parking is free in Santa Cruz County park and ride lots, and that publicly owned real estate does not generate property tax revenue for the local governments.
I'm simplifying greatly -- not every Highway 17 bus passes through Scotts Valley, and the bike racks aren't generally used to capacity for every trip -- but I think I make my point that spending resources for bike transportation can be cost effective for the transit operator and beneficial for all bus riders. It lets the transit district design a smaller parking lot and makes more parking available for the riders who drive to the bus station.