The Beeching Report was not written when the roads and city centres were anywhere near as congested as there are today. Maybe the findings of the Beeching Report are still true for the West Country but for the areas around Manchester, Liverpool, Leeds, Birmingham & Wolverhampton saying its findings are out-dated might be a understatement. I did watch a program Ian Hislop did on what effect the Beeching cuts had once and I do remember it being mentioned that everywhere that was losing their station had a local bus service instead. Unfortunately, that doesn't apply to all places Northern have reduced the train service to e.g. Plumley has no bus services, we need to catch a train to at least the next station in either direction before we can catch a bus.
There is a massive difference between small villages and conurbations with poor rail services. One could very well justify a rail service, even if not of the traditional heavy rail type (c.f. Midland Metro), the other is going to need a massive amount of subsidy no matter how high a percentage of the people who live there use it.
With the benefit of hindsight, no-one can seriously suggest that the Beeching cuts didn't go too far. However, some lines were closed for justifiable reasons, and wouldn't be reopened even if you could do it for the same amount it cost to build it back in the 19th Century.
Coming back to the point, most of the branch lines that closed simply were not sustainable and still wouldn't be so today. It would be a political choice, not an economically justifiable decision, to reopen such lines - see, for example, Wisbech.
There are very few parts of the country that aren't within a reasonable rail-heading distance of a station. I think that kinda tells you everything you need to know about how this country's approach to public transport tends to end up working out.
Network Rail have recently done some track replacement work around the Knutsford area. The Highways Agency recently built a new A556 link road between the M6 and M56 junctions near Knutsford. I'm sure Network Rail took in to account the freight usage as well as passenger usage when deciding to do the track replacement work and I'm sure the Highways Agency weren't just thinking about cars going between the M6 and M56 but considered there were a lot of lorries as well. That's the thing quoting subsides for passenger franchises ignores - some rail routes would be well used freight routes even if there were no passenger trains and some roads would be well used by lorries even if everyone stopped driving cars. I don't know exactly how Network Rail get their money but do GWR, for instance, fund 100% of track work if they run passenger services on a Cornish branch line which no-one else uses or do they just pay a toll charge proportional to the size of the train used? If it's the latter or something similar then it's a flawed system and what you've said about passenger subsides is just a figure used for political purposes.
Track charging is a fiendishly complicated subject that has changed many times over the years. In essence, passenger TOCs and other companies with fixed-term access agreements pay a fixed "track access" charge which contributes to the cost of keeping open the pieces of the network they run over. All train operators then pay a "track usage" fee per mile based on trains that are actually run, which is intended to cover the variable costs NR incurs through the train operating.
All sounds hunky dory, but in fact even the comparitively dear fixed access charges rarely cover the cost of maintaining routes, especially not the cost of renewals. So when calculating true passenger subsidy you can't just go off the amount that the franchises pay the government or vice versa (as it used to be). You have to include an apportionment of the rather sizeable grants paid to Network Rail by the DfT each year.
So the answer your question, GWR pay a contribution towards 100% of the costs of maintaining a route like the Falmouth branch as they are its only regular user. No doubt the true costs of maintaining the route are far more than this. It's not at all a political argument to point out that such routes are heavily subsidised by virtue of the fixed track access charges being less than the cost of maintenance.
Again coming back onto the topic, it's no surprise that Northern are the joint highest subsidised TOC. They are the only permanent operator over significant portions of track with low passenger usage such as the Cumbrian Coast line. Passenger revenue is barely going to cover the cost of operating the train, let alone maintaining the infrastructure.
Relating to this to the timetable fiasco, you would have to subsidise such operations even more to get back to a reliable and normal timetable; as I said, that it's going to be difficult to justify. It's difficult to sell a headline of "£50m spent on making 5% more trains actually run".