UK railways have been chronically mismanaged for years. Better comparison would be against other European countries.
They could probably also do it by whacking the extremely wealthy landowners surrounding major train stations with an extra tax.
After all, if the train station made your land valuable, you should be paying for that. In Japan this helps pay for infrastructure. It's practically criminal that in the UK it does not.
(anyone in the age range eligible for InterRail, I would highly recommend spending a month travelling the railways of Europe)
In the UK we have decided to go for lower taxes and lower subsidies. We do that while still subsidising lines that are good for the country but not profitable (old mining towns in south wales which would collapse if people couldn't commute to Cardiff etc, cornish rurual lines which attract tourism and offer transport for local residents who may not have 1 car per adult, etc). This means that on the profitable lines which would make commercial sense (say Manchester to London, or some London commuter lines) we have to charge more.
Remember commuter tickets are twice the price of business tickets - as they are paid after income tax (which varies from 33% to 60%). When I was offered a job based in the office, I wanted an extra £10k a year for the commute -- £2200 for the ticket, £3300 for the extra tax to pay for that ticket, and £5k for the time out of my day. They decided that I didn't actually need to be based in an office after all, and I go (to that one) about once every 3 months, which costs them £20 return (but would cost me £45).
This is offset by the massive discounts. A season ticket from Nuneaton to London, 206 miles a day, about 1 hour in each direction, is £9000 a year, for 230+ days of travel, or 47,000 miles. 19p per mile. If you're willing to take a little longer and travel on London Midland it's £6500 per year, 14p per mile.
On the other hand, a day trip from Nuneaton is £154 in peak time, £104 on the slower train. That's 74p per mile - 3.5 times the price of the commuter.
There is a profit margin to be made on any savings, I'm sure that if Stagecoach or First or whoever could cut costs enough to make more money they would. We have very old infrastructure, laid down in the mid 19th centuries, and very crowded lines. Building a new line is a mammoth task, and expensive, as we've seen from HS2. Rail staff are hardly cheap too - a virgin trains driver earns £51k, top 10% of earnings in the country.
The media has driven this culture of people believing in 'rip off Britain'. If people were commuting 100 miles a day for the cost of a cup of coffee they'd still say it was a rip off (although oddly it would be the commute, not the £4 latte)
Two stops in from where I get on the train fills up dramatically and there are often people standing.
Interestingly, I can take a 3.5-4hr train from Penang to Kuala Lumpur for $12, made by Siemens I believe, traveling faster than the Pendolino/Voyagers, and with a similar level of comfort (I do think the seats are bit narrower though), so in comparison I consider the UK crazy priced unless you get some off-peak deal (still not great).
I suspect if still subsidized then it's probably very inefficient, I dont know but I certainly dont feel good paying the train ticket prices in the UK even the off-peak saver.