I'd second everything Bob said. I rarely use any public transportation here in the US and was also worried about the language barrier before I went. It only took a few trips for us to feel comfortable using the Shinkansen, subways, buses, etc. in Japan.
Of course, it always helps to have your own map and information. It will really speed communications along if you know the station you want to get to, or at least the name of the area (Harajuku station, Shiodome station, etc.). A map helps too, of course. Maps were found at most info booths at major stations.
Assuming you get a JR Pass, I'd make a suggestion though. If you're going somewhere using the Shinkansen, consider making the effort to find the local JR reservation office in the train station. Sure, you can hop on the non-reserved cars without paying, but I found that often-times, even not during rush hour, those cars grew quite crowded, sometimes filling to 'standing room only.' Reserving a seat not only guarantees a seat, but they also are good about telling you which platform to go to, if you have problems with that.
A few times we needed to use local transportation that our JR Pass didn't work on, but the problems were easily solved, to put your mind at rest:
Okayama - The local tram was useful for getting from the station to our hotel, and around the city in general. We just followed what everyone else did. Grab a ticket when getting on, dump 200 yen in the machine getting off.
Kyoto - Local subway - The subway ticket machine at the main station had some English, and the maps near it told me how much to put in, so not a big deal. However, the machine at the other end didn't have English, so I did have to ask a station worker for help. I basically told him the destination (JR Kyoto station), and he helped me push the right buttons.
Tokyo - Local bus from station to the Tsukiji Fish Market - We just got on and watched what everyone else did, just put some change in the machine (200 yen, I think it was).
If you get lost, I found that asking the people at the little window right at the ticket gates helps. They always knew enough English to understand what I was asking, and most (not all) were friendly. More than once I even encountered Japanese people asking them for directions.
Again, don't worry too much, it shouldn't take long before you feel comfortable using the trains.
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