Nice article and it does paint an interesting picture of what is possible. However, doing snap shots of particular cities and even areas of cities can give a false impression of the state of bicycle commuting - even in the showcased cities.
For example, I loved the pictures of Kyoto. I live in Japan for 7 years - but I lived on the island of Okinawa. We had great roads and it was not a particularly dangerous area to ride - but very heavy traffic and traffic circles were a challenge. Fortunately, the speed limit was 50 KPH on most of the island. We were expected to filter to the front of the traffic lines at lights and I was often allowed to pass and weave through stalled traffic with a wave, flash of the lights, and a smile. Eye contact was real important.
Italy, where I lived for 3 years, was a different ball of wax. The drivers were, for the most part, careful around bicycles. Towns were pretty easy to get around in, but the streets in the area I lived were often cobbled - and that can be a challenge. The rural roads were narrow with no shoulder at all in most places. The better traveled roads and strada had wider shoulders but the vehicular traffic was moving at pretty high speed so the cyclist had best hold a pretty good line. I lived near Brindisi, on the Adriatic, and the area was pretty rural. It was pretty cool having a farmer wave at you to jump behind his APE cart and motor pace (draft) on the way to work!!