I've seen enough trigger words to set me off now, although I think the Yes Minister plot is still a useful summary.
I can't speak for the DfT, but I have some experience of working with another ministry much in the news of late. It sounds as if they have -synergy-.
Lets start with the Civil Servants....
The role of the civil service within a ministry is to implement the legislation, policies and other business for the government of the day. It's there to provide an element of independence and continuity within a system that can in theory change our rulers every couple of years.
With increasing overt or implicit privatisation of many services, the role of the civil servant has changed. Instead of being responsible for service delivery, they have become responsible for overseeing those who do deliver, in theory to ensure that the taxpayer is receiving value for money. Unfortunately the wheels turn slowly and many organisations and individuals within the civil service don't understand their changed role. They mistake interference for oversight and micro-management for effective management. Ultimately, they're frightened of looking irrelevant but don't have the skills or remit to become effective.
As the civil service is an agent of continuity, the way it performs its business is largely process-driven, rather than results-based. Because of this, it attracts people who are by nature conservative with a small 'c' and usually not of an innovative or creative bent. A civil servant will gain promotion and a comfortable pension by following procedure. As soon as a civil servant is called upon to make a significant or difficult decision, they know that a wrong choice may scupper their climb up the greasy pole. Couple that with a culture that doesn't promote innovative thinking or attract those capable of it, and you have a recipe for stagnation.
I know many civil servants and some of them are clever, innovative and driven by results. They are mostly unhappy in their jobs.
Procurement now.....
In my own particular industry and back in the dawn of time, there was something called cost-plus. A ministry would ask for something, a manufacturer would try and make it (and occasionally succeed, but more often than not piss the taxpayers' money up the wall) and then get paid however much they'd spent, plus a little bit extra.
This approach was expensive, open to abuse and encouraged profligacy by the manufacturers. So the government of the day decided to change things, but change them so radically that they effectively crippled the procurement process. In essence, the government tried to transfer nearly all the risk for any procurement on to the supplier while (and this is key) retaining a disproportionate amount of control over how that procurement might be delivered. It's like walking into a restaurant, standing over the chef while he or she cooks you steak giving instructions and then refusing to pay because the streak was 'rubbery'.
This situation persists today, and it seems from Dom's description of the railways that the approach has caught on. Certainly its not a bad summary of rail privatisation. Ultimately the suppliers (not entirely innocent themselves) still have to make a profit. Any procurement process becomes bogged down (ref civil servant mentality above) in a battle between the supplier and the government, with each believing that they're being screwed over by the other. Once the contract has been signed, the supplier will try everything legal and beyond to manage their own risk, usually at the expense of the end user. Meanwhile, the government and civil service will often step in, still believing they have the right to tinker without having to take any responsibility for the cost or consequences of their fiddling.
And all the while the money-clock ticks over. Not an effective way of making stuff happen.
Finally the Government....
I've never been to P&L and I'm not going to start now, so I'll keep this one short and point out that I mean any government of recent vintage. Today, the country's perception of the government is driven largely by the media. The popular media is a very dirty lens through which to view the goings on of government, and it's controlled by very few, very powerful individuals. These individuals are generally of conservative outlook and have many vested interests. Any radical thinking by a government that steps away from the narrow world view promoted by the popular media, such as a wholesale change in transport policy, will be stillborn. Even if a government had the motivation (and I don't believe the present or future lot do) there is no benefit to the government to make serious decisions about, in this case, transport because it will be presented to the people in such a way as to damage the their chances of re-election. At best, we get tinkering that keeps below the media radar. Only when a government is motivated by political dogma that aligns with the interests of the media owners does something happen. Like rail privatisation. <irony>Chapeaux</>
So to summarise, we have a government and civil service whose best interests are served by inaction and a procurement mechanism for public works that cannot function properly within a capitalist society.
I think that counts as 'not a one word answer'.