Many young men (and women) live in company apartments or dorms. I know a nurse whose hospital provided this for free and a Mizuho banker who had to pay 12,000 yen a month.
Also, almost every job pays transportation (if you choose to commute by car, you get a flat rate for it). Many people either skim money from this (such as using one train line but taking another) or extend it to other stations (that they frequently go to).