There are other issues involved - key money, cleaning deposits, guarantors and laws which lay heavily upon the side of renters - such that landlords can be very difficult to work with. It's not uncommon to have them say "sorry, no foreigners". I'd imagine the same stigma holds for other groups of people.

Tokyo is pretty expensive, and transportation is also really expensive. I'm paying about $550 for rent at the moment (11m^2, shared restroom/shower) "inside" of Tokyo. I got really lucky finding my place though, most equivalent places around here go for at least $100 more a month. If I were working in Shinjuku, it would probably cost me $100 a month for a commuter pass. Internet is pretty cheap though (you can get a home line for about $30 a month).

Still seems to be a bit of a losing proposition, though.