A couple quick points:
1) If anyone ever comes up with a location-agnostic language icon for English, I'll implement it in a heartbeat. Using the Japanese flag for Japanese seems very safe.
2) Based upon the traffic to my site so far, all of my English-speaking audience is from the US.
3) The only time you'd be seeing the "US" flag (which does represent en-US, in my case) is when you're on the Japanese version of the site.