Couple that with the fact that Hokkaido is as far north as you can get in Japan (as far from Tokyo and other major population centers further south, so there may not be missile defense systems there. Israel's Iron Dome only has a range of 70km, so I doubt, even if Japan had better technology, that they'd have one of these set up everywhere across the islands.
Being that Hokkaido is so far north, if you look on a map it's very very close to Russia. Not knowing the exact trajectory that it took, it's plausible that it went over Japanese airspace but was obviously not on a trajectory to impact the island itself. The article doesn't say where it was headed, just that it was in Japanese "airspace", and that it landed off the coast.
So plenty of reasons why it wasn't shot down. I'll add one more: the last thing you want to do is try to shoot down a test rocket and fail. Because if you fail on the test, the enemy will be more willing to believe you'd fail on the real thing, too.
Shooting it down could reveal anti-missile capabilities that may be saved for a more serious impact threat.
Depending on where the missile is projected to land it might be a better idea not to shoot it.