Southern don't make money from the Metro services within London as the can't set their own fares as they're done with the Association of Train Companies for paper and Oyster/Contactless. They can make money out of London to Brighton for example.

It's also part of GTR (Govia Thameslink Railway) which is under a management contract with the Department for Transport who are dictacting the levels of service they can provide, so any revenue earned goes back to the Government.