...is that most Japanese seem to view it as precisely that: an aspect of Japanese culture. Practice of various Shinto ritual behaviors is viewed as being "part of what it is to be Japanese" rather than something reflecting literal belief. Few Japanese I've met (and I've also read up on this matter a bit, so my take goes a bit beyond anecdotal experience) profess belief in any sort of "magical" upstream causal factors behind physical phenomena.

That is, obviously, why Shinto doesn't find itself in opposition to scientific knowledge.