For example Yamaha Motor company in Shizouka pay employees who cycle an extra Y1000 per month. Okuchi Shuzo a producer of shochu in Kagoshima offer bicycle commuters Y10 per kilometer. Nobody it seems is addressing the issue of showers and parking for example.
While we have no showers at my company, and there is not a lot we can do about it, we are able to park our bicycles inside the building at no cost. In addition to this anyone cycling to work still receives their full commuter allowance which nets me an extra Y10,000 per month.
We don't consider that a special benefit, just fair and equal treatment.