It's always nice to shed some light on the real-life situation, rather than talk only about the good and best of things. It helps to understand.
Frankly speaking, bicycles in Japan are not the best behaving vehicles in the world.
(Before going any further, this does NOT mean that cycling in Japan is dangerous, that's another story.)
There are many cyclists in Japan that understand the rules and etiquetts of the bicycle, are conscious about where the bicycle fits in the traffic infrastructure, and obey traffic laws that apply to bikes. Unfortunately, there are also many bicycle riders that do not.
The majority of hobby cyclists fit into the former category, whereas the majority of other cyclists fit into the latter.
Elderly moms and pops who's riding habits soaked in their body in the old days when they didn't have to care about heavy traffic and co-existance. Teenagers at the age when "going their own way" is the cool thing to do. High school girls that can't put their text-ing (and iPods) away while they ride their bicycles. Mothers with small kids, who just want to get there choirs done as soon as possible, before the child starts crying. Most of them ride on the "mama-chari", and ride around the neighborhood shopping streets in living areas, so visitors may not encounter them in central Tokyo.
These "latter" type people exist, and are the ones that run through stop signs and red lights, ride on the opposite side of the road, making sudden manouvers surprising cars and pedestrians, and ride on the sidewalk violently ringing bells scattering people away to the side as if they are the king of the road. All of these behaviors are illigal by the law, but can be seen on a daily basis.
Now what kind of atmosphere allows this in Japan?
In my opinion, the biggest cause for this is that though bicycles are legally categorized as light vehicles (hence must abide by vehicle rules), they are not treated so in real-life. People are used to categorizing bicycles closer to the pedestrian than vehicles, within the big picture. People using bicycles for everyday utility treat them as "geta", or clogs, with the mind that they can be used easily like your feet, not being tied up to traffic rules. There are actual statistics that show more than half of people were not aware they were violating traffic laws, and were not aware that bicycles had to follow traffic laws in the first place.
Then, there are the authorities that also have a half-way thinking regarding the positioning of bikes, proofed by the existance of a rule that allow bikes on sidewalks with pedestrians. There are so few bike lanes that if existed, would designate bicycles as independent vehicle category with their own place to run. Instead, there is a widespread notion that bikes should run safe on the sidewalk as part of the pedestrian infrastructure.(which in fact does not align with the actual traffic law that say bikes basically belong on the roadway.)
Every cyclist in Japan, old,young, hobby cyclists to mamachari riders... has to realize that bicycles are not "getas"(part of pedestrians) but are vehicles. This awareness will become the root of good cycling behavior, leading to a good reputation for bicycles, and a good traffic environment for all. This change in notion will require education and evanagelism, which the social system has the responsibility of doing.
By the way, here's another interesting article I found.
Dannycho.com : Tokyo Bicycles - http://www.dannychoo.com/post/en/857/Tokyo+Bicycles.html