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This can't be understatedThat's a bit overstated... :]
Japan's phone manufacturers concentrate on the Japanese domestic market, so there's a great deal more choice in high-quality phones in Japan than in most other countries.
Samsung is not "special" like Apple is, in that their products aren't higher-quality / more functional / better designed than the (mostly Japanese) competition, so there's no real reason why Samsung should be ahead of other companies. They may have some price advantage, but price is generally less important in Japan than it is in other countries, and is often rather obscured in phone contracts. Samsung coming in 4th is actually a vote of confidence.
To the degree there's a bias in Japan against non-Japanese products, I think it's in most cases less a case of xenophobia, and more simply a higher degree of trust in Japanese products. This isn't entirely illogical either, as Japan does have a very good record of building high-quality products. Japanese can be very, very, picky, about both quality and style. [This is one reason Apple does very well in Japan.]