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.
You argue that most murders are criminals killing each other. Suppose you're right. So let's look at robberies instead. Those are primarily directed towards random people not towards other criminals.
The safest US city in that respect is Irvine with ~20 per 100k (https://en.wikipedia.org/wiki/List_of_United_States_cities_b...). Irvine is indeed a very safe city, and I doubt parents would be concerned too much with letting their kids walk to school (if only the school was within a walking distance away).
Now move out of Irvine. Pick a city. San Francisco is ~360, NYC is ~160, Seattle is ~210. Even Mountain View, near Apple, Google, and many other high tech companies is ~60.
And btw, people in Tokyo generally do very little protect themselves from violent crime, since it's so rare. They walk around late, alone, often drunk, paying no attention to their surroundings. I'm pretty sure if people behaved like that in SF, the robbery rate would jump significantly.
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.