The Zones are hard to compare. For instance in Tokyo, on average the vast majority of the rides I took were about 160-190 yen each way, so basically $1.60-$1.90, on the Yamanote line itself the most expensive is 260 Yen. I definitely spend less money in a Month on the train in Japan than I do on the Subway.

Rides that cost more tend to go further out than the Subway system and would be more comparable to the LIRR or Metro North. But its not a perfect comparison and there are certainly specific places where it could be more, and not every train company has the same price structure.