The big difference is not for-profit status, but the fact that Tokyo's and Hong Kong's subway operators own much of the property around the stations, and make a ton of money leasing it:
http://money.cnn.com/2015/03/30/news/hong-kong-mtr-subway-pr.... Economically that makes a lot of sense. Transit infrastructure creates a positive externality: it benefits not only the rider, but the shop or office that the rider goes to. NYC's MTA can only recover from one side of the transaction: the rider. JR and MTR, as major landlords around the stations, can recover from both sides, capturing some of the positive externality.