Personally I think there needs to be a review of the lines which require the highest subsidy and that would include Network Rails costs whether there is any freight on the line, and a look at all the options such as improving the service, do nothing, ways to reduce costs, possible closure, and replacement with a connecting bus service, and if its replacement with a connecting bus service, then that should be part of the franchise agreement which would have go through the same closure procedures as closure of a Rail Service.
I'm sure the above wont be popular on here but I don't believe all existing lines should carry on regardless, the money should go where its most cost effective, Unfortunately Governments with Balls to close a Rail Line's seem to thin on the ground at the moment.