Anything in Japanese only obeys the rules of whatever romanization you've chosen. But if you choose a romanization, apply it uniformly. Your question doesn't really make any sense.
But if you're asking if Japanese people use Hepburn romanization, no, they don't. Everyone in Japan is taught kunrei-shiki in school in elementary school. Kunrei-shiki is
very different from Hepburn.
Kunrei-shiki romanization - Wikipedia, the free encyclopedia