To be clear, rail fares in Greater Manchester are regulated by Transport for Greater Manchester, and that's not the same as subsidising. They also regulate fares for Glossop, Hadfield and Dinting. Ultimately most fare control for regulated fares sits with the Department for Transport - witness a few years ago when the Department for Transport decided that off peak tickets would not be valid between 4 and 6:30pm. Transport for Greater Manchester was not involved in that decision.
Transport for Greater Manchester do subsidise some fares - things like over 65s getting free travel on trains and trams, as well as buses.
Fares for New Mills are officially set by Northern Railway - and that basically means where fares are regulated, they are controlled by the Department for Transport.
Basically unless Northern decide to reduce the fares out of the good of their own heart, nothing will ever happen, because the DfT certainly isn't going to do anything.