Is Japan really a bicycle friendly country?
It is indeed. However there are some particular rules that you should follow when biking and they are quite strict and may seem strange to a foreigner. For example, I found it strange that you cannot attach your bicycle to anything when leaving it on the streen, the maximum you can do is to put a lock on the wheels and leave it (but someone could just carry it away, right?). There are also a bunch of rules that you should follow on the road. What what difficult for me was that you can't wear headphones while biking. It makes sense, but comparing to rules in France where there are no rules really, bicycles don't even stop at red light (because the rules for car drivers are so strict that they feel that it is their responsibility to ensure that nothing bad happens on the road), it was kind of strange.
Japan is bicycle-friendly, and they are widely used by university and high school students, and mothers with small kids. Some rules regarding bicycles were not strictly enforced until recently. Those are:
You can't ride bicycles on the pavement, unless you are a child or are carrying a child.
If you are cycling on the pavement, you have to be riding on the left side of the road so that you can get on the road when there are too many pedestrians.
These got strictly enforced because of accidents involving old pedestrians.
If you are riding a bicycle without a lock or with a broken lock, you might get checked by the police (they explain this reason when they stop you). Stealing bicycles is one of the common crimes; My neighbourhood has 30,000 residents and about four bicycles get stolen each month. These are usually found somewhere after a student takes it for convenience; otherwise they end up in a South East Asian country.