If subsidy free profits are the sole directive for rail operations in future,
1. Remove it from services category, separate rail ministry and UPSC service cadre both not required.
2. Avoid politicizing the decisions like distributing trains, facilities.
3. Increase fares/cut subsidies directly by informing the public and not through back pocket.
4....
more... Protect rail properties like precious land from encroachers, tracks from protestors, coaches from stone pelters, more than own personal property.
And if cabinet shows its inability in doing so, in the name of public service or due to their vote bank appeasement mindset, then better sell it out to tata /any private party.
But playing this dual sided game of subsidy loot and poor service and then crying foul is not welcome at all.