That 3.5 is almost without exception crime-related. Your odds of being a victim of extreme violence even if you weren't involved in what started it are effectively zero. Miyazaki prefecture probably experiences this same phenomenon. If even that is too much for you to risk, there's a city a couple of hours away with a population of 100k and a murder rate of 0.00. We haven't even mentioned the Japanese tendency to only prosecute slam dunk cases.
The major point is that although Tokyo might be "safer" on paper, the risk profile of letting your kid walk around Tokyo vs. letting your kid walk around the city I mentioned is pretty much the same in practice, and this goes for thousands of American cities. There are millions of Americans who could let their kids walk around their community and not have to worry about them being murdered or seriously assaulted.
The major point is that although Tokyo might be "safer" on paper, the risk profile of letting your kid walk around Tokyo vs. letting your kid walk around the city I mentioned is pretty much the same in practice, and this goes for thousands of American cities. There are millions of Americans who could let their kids walk around their community and not have to worry about them being murdered or seriously assaulted.