It's the profit they made over and above the subsidy paid on ticket sales. Other TOCs also pay that, plus they pay a franchise premium, they pay full track access and are not allowed to defer work committed to under a franchise agreement. In effect as both Network Rail and DOR (East Coast) are Government owned companies, the taxpayer is subsidising this operation far more than the published figures show.
 I have no problem with that, but it should be remembered that National Express and GNER^▸ (Great North Eastern Railways) before them were making profits and paying large sums to the taxpayer as well. In GNER's case the parent company, Sea Containers, ran into trouble totally unconnected with the railway and could not pay the annual performance bond.  Could another operator have bought the franchise from Sea Containers?  Ask the DfT^» (Department for Transport - about). I personally think it tragic that GNER, are no longer around.

National Express made their profits forecast when taking over the franchise, but the recession occurred and the forecast was too optimistic. They were making money, and paying the Govt.  but not enough to meet the agreed level. 
Back then the DfT civil servants were basically telling operators bidding for a franchise that they had to pay the Govt. a lot of money for the privilege of doing so, and that they had to guess what big figure was in the mind of the Treasury and get a bid that was either very close or exceeded it.

Those who feel East Coast is justification for running a 'nationalised railway' are comparing oranges with apples in my opinion.

The franchising model is now a lot more mature, the taxpayer is making a profit overall, the DfT have (finally) got some expertise and set up a separate railway section, plus bidders are more realistic. 

This new contract for FGW^▸ (First Great Western) will take into account the risks inherent with running a service along a giant building site, plus the introduction of the new IEP^▸ (Intercity Express Program / Project.) trains and electric commuter stock in the Thames Valley, the transfer of some services and staff to Crossrail, and the move westwards of the DMUs^▸ (Diesel Multiple Unit) currently based at Reading, which themselves have to undergo a rebuild to make them fit for many more years service.  We still do not know for certain what will run the services to the far South West. Life extended HSTs^▸ (High Speed Train) were the original intention, but the costs could well see that idea scrapped and either more IEPs with more diesel engines installed, or class 222s transferred as the Midland Main Line is electrified. (I'm hoping for an HST solution, still the premier train.)

In answer to the question above, the locomotive D7 Ingleborough, which I first saw 45 years ago on 3rd October 1969 as it passed through Peterborough on a coal train from Toton to Whitemoor.

Delay / Repay on a line that will become one very long building site?  That will be some hard negotiating.

There is of course the practical common sense view of electrification, and then there is the entrenched 'Ivory Tower' view of people far away who work in the DfT^» (Department for Transport - about) and generally get the 1630 out of Waterloo on a railway which has enjoyed massive investment over the years.    Sorry, I get a bit jaundiced dealing with DfT decision making. The DfT civil servants carried out the assessment assuming no increase in passengers or services.  Sorry, but we've known for over 40 years about the 'Sparks Effect'. Put on electric trains, running frequently and passenger numbers soar.

Common sense would say that the wires should go to a major nodal point on the route, and that is neither Newbury or Bedwyn, it's Westbury. Just a few miles from the major National Grid feed in point near Melksham for the Chippenham to Bristol section. Whip the wires up through Trowbridge and Melksham and there is a major diversionary route fully wired. 

Using normal 110 mph class 387s Westbury and intermediate stations can be reached just as quickly as Bedwyn is today using 90 mph DMUs^▸ (Diesel Multiple Unit) which are nowhere near as fast accelerating from rest.   Claire Perry is the MP^▸ (Member of Parliament) for Devizes as well as a Transport Minister, but this does not give her any extra influence over this, but it certainly helps to have support for the idea in high places.

It's all down to the bean counters in the end and seeing as GWML^▸ (Great Western Main Line) electrification has already creeped over some red lines it will take some innovation to win through.

There is some hope. First Group run Hull Trains. As part of a conglomerate they have offered to finance the electrification of the line to Hull from the East Coast main Line. The latest information was that this offer was on the verge of being accepted, a UK^▸ (United Kingdom) precedent will be set. Given the size of the market in Wiltshire and from services connecting in from other areas, that could possibly work here.

As an aside, one of the major electricity suppliers in the late 1990s offered to electrify most of the old BR^▸ (British Rail(ways)) Western Region in return for a 20 year supply contract.  Railtrack said no thanks.  I wonder how that could have worked out? 

There is a large market beyond Bedwyn, the few HSTs^▸ (High Speed Train) that serve those stops at places like Pewsey see plenty of use. Put on the trains and the passengers will come.
 

BBC^» (British Broadcasting Corporation - home page), how many times

It is NOT a franchise extension.    It is a direct award on completely new terms.

and yes, it is legal under EU^» (European Union - about) rules.

The details will be made public once negotiations are completed, and as yet, they have not been. The BBC jumped the gun having learned of a meeting that took place 48 hours ago. There are still some things to sort.

Of course East Coast does not have to pay it's way in the same way other TOCs^▸ (Train Operating Company) do. No franchise premium, cheaper track access charges, and they have deferred a lot of work that other franchises have to undertake. It's been a 'holding exercise'.

There is a lot more to look at than just a simple subsidy profile, and the Govt. makes more out of franchising than anybody else, especially the operators.

To put some perspective on this plan. It's anticipated this station will have to handle 250,000 passengers a day.
That would put it up amongst the top 20 busiest stations in Europe, and very near the top of the table in the UK^▸ (United Kingdom).