Also, when I go to my Japanese wife's parents house, the whole family often has natto on top of rice as part of breakfast, often with chopped onions or thin sliced okra on it.
And, I myself came to like natto after forcing it down a few times at breakfast to be polite to my host family the first time I visited Japan 25 years ago.
So I'm pretty sure it is common to eat natto for breakfast in Japan. There are surely some people who hate it, though -- but lots of kids hate takoyaki, too.
Lots of Japanese like natto, lots of Japanese don't like natto. Go to France and you'll find the same thing is true of blue cheese.
Maybe natto is slightly more popular in Kanto. Maybe it wasn't common in Kansai 100 years ago and that's how the myth started. But let's stop staying Kansai people don't usually eat natto, when it's plain to see that's not the case.