Most of the moaning comes from the press. Unfortunately bad news sells, good news does not. If the railways were that bad, they wouldn't have growing passenger numbers. But people like to exaggerate things out of all proportion, such as expensive fares.
For example according to the head of Virgin Trains, only 5% of people are paying the expensive tickets quoted by the press, often businessmen on expenses. The vast majority (around 80%) are travelling on reduced rate or advance tickets. I came back from Birmingham on Sunday for just £7 to London, which compared well with my bus ticket (frequently held up as a cheap form of transport) which was £4.10 for 8 miles. The average rail fare BTW is around £4.50.
It's not to say that the railways haven't got challenges. The West coast main line upgrade did an enormous amount of damage to the industry over questions of value for money. And looking at the WCML over the weekend, there is still an amazing about of work to do, with much 60s signalling remaining in the West Midlands, Stafford, Crewe, Bletchley, Watford Junction, Macclesfield, Stockport areas. The bottlenecks of Birmingham New Street, Stafford, Crewe still remain, and much of the line north of Weaver junction is as it was, save a few line speed upgrades (often by selective track replacement and moving the odd signal). The French built a whole HSL for 1/3 of the cost.
I would say roots of the problems are in political interference and red tape rather than a problem with the system itself. If that wasn't the case, the two countries with the biggest rail use in China and India wouldn't have that crown as wages are generally a fraction compared to here.
Timekeeping, certainly the railways have the best record, a very unreported fact and generally they have the best customer satisfaction too. Upwards of 80%, whereas some quite famous transport concerns its nearer 50%.
The two challengers for the future remain PR (getting their message across which they do VERY badly) and costs.
That said, its often referred as the railways costs billions as if cost are way above anything else. IT databases (a bunch of code) is also costed in billions, and we spend around £250 billion on the road system per year in terms of vehicles, running costs, insurance and so on. Total revenue for the passenger rail system (including subsidy) is about the same as Tescos for 1 week, or British Airways for a year, an airline with the same number of passengers as Mersey Rail. So we're not spending the huge amount of money people think, indeed, even someone as pro rail as me, has probably spent 25 times more on cars than train tickets! tut tut!