It only costs that much if you're staying far away or going pretty long distances. I stay in a station pretty far from Central Tokyo (past Kita Senju on the Tobu line) and to get to somewhere like Ginza costs less than 400 Yen, which is about $3.75. However, a chunk of that cost is due to Tobu, and if I was staying in Kita Senju or Ueno my trip would only be about 200-250 Yen.

If you are going from Kita Senju to Ginza then you would be using the Hibiya line. That trip will cost 195yen. Which is the same price for going all the way down to Roppongi where Google is. The Tokyo Metro and Toei lines tend to only have two or three prices depending on distance. This is why going two and three stations almost always costs the same.

Since employers always pay for commuting costs a regular working person spends very little on train tickets day to day. Me and my wife spend about $100 per month between us. With our companies paying a further $70 per month for each of us for our passes to work.