Just a thought that occurred to me recently: Although we may not think of it, we are transliterating as we write Japanese with our computers. An overwhelming majority of people use the standard QWERTY key layout (even in Japan), and as we use IME or whatever input method, we are typing a romanized version of Japanese.
When I am actually writing Japanese words in romaji, I use Hepburn, but when I type using IME, I use whatever method allows for the least number of keystrokes.