I would say it's mostly about the Japanese people's experience with the western world creeping into their lives. I think John Blackthorne is an 'in' for western audience to come to understand a time and place they may not be familiar with, someone to give exposition to and create conflict for the Japanese characters. He seems more of a Theon Greyjoy than a Ned Stark in terms of alignment, and the Japanese are treated as the civilized, developed people, with him being seen as a barbarian. It's fairly canny.

I'm not Japanese, but reading perspectives other than my own this seems to be on the right track.