The US demilitarized Japan after they were defeated in WWII, with the Japanese preferentially surrendering to the US to hope for a better deal. The US then established a bunch of bases there. The point of this was to (1) prevent Japan from remilitarizing as its own imperial power and (2) use it as a forward base against the USSR and China.

The US is still using Japan to do this and important segments of the Japanese ruling class are trying to remilitarize Japan itself, both coordinating against China.

Finally, Japan has questionable sovereignty. Japan's economic downtown in the 90s was "synthetic" in the sense that it was created by US-led fiscal policy and not any "natural" result of their economy. I'm sure much of its political class is aware of this. And they are still basically militarily occupied by the US given those *massive" bases, many of which are very unpopular with the locals. Just ask Okinawa.

And again, this is a plane doing a small toe dip on one route vs. long-range missiles designed to be able to carry nukes. Incredibly disproportionate.