Religions could be powerful agencies to pass a certain set of cultural or social lessons to the following generations. So could be political parties, maybe. Even in a place where those kinds of cultural or social agencies seem to have clear frames and bodies to unite people under their own values and ideas, still people never stay at the same spot. They flow, thus forming new cultures (in the same current).
In this country, religions don't have a strong influence in formal fashion anymore. I wouldn't say they're gone, but it is true that a lot of people are not religious. Nor do they have clear political views either. Compared to other countries, people are way less interested in politics in this country. They do know what media say, but they don't talk about it among themselves.
The tricky part is, that even after losing the shape of religions and stuff, modern cultures or people's mind are not built on nothing. Morality and values are taught to young generations in messages at school, family, and society itself, while interacting with older people. And the problems is that those lessons don't make sense, lacking the basis, and we don't know where they came from. We just do it because it "feels" right and we are taught to do so.
Not making sense is not just the problem foreigners find when coming to Japan. It's also a bothering aspect of Japanese "culture" for people in this country. We don't know what Yamato-damashii（大和魂）exactly means, we don't know why we have such a strong seniority system all over the society... well, we know that it was originally adopted from Confucianism, but that's not an explanation "why" we have it now.
I don't like blaming people for not being open to other cultures or being proud of their nationality or whatever. I just believe we should start questioning about and talking about our own "cultures". Where did it come from, and where is it going? There are so many things in this society, things that don't make sense.