I think the point (made in the text prior to that chart) is that passenger km went up 59%, with cost per passenger km stayed largely static (down 3%).
You'd expect a much greater drop in unit costs for a network carrying 59% more passengers with a similar-sized train fleet.
The figures include some large Network Rail costs (enhancements etc) which don't usually figure in TOC franchise subsidies (the NR direct grant policy).
But it's why NR debt is now £50 billion or so, the interest hitting industry annual costs.
This was in the Interim Report:
We consider that there is considerable scope for the overall increase in expenditure to be reversed. Since 1996-97, although rail passenger-km have increased by 59%, there has been little or no improvement in the total cost per passenger-km, which is remarkable in an industry with relatively high fixed costs. Figure 1 below shows that, while there have been reductions of between 1 and 3% per year in train operating costs and infrastructure operating and maintenance expenditures, these have been largely offset by increases in renewals costs (largely driven by increasing volumes) and enhancement expenditures to accommodate the additional demand.
Of course, the costs were mostly for the 2000s and are now 8 years out of date.
The report has a lot to say about industry organisation and incentives, franchise lengths etc.
The new Williams report is going to re-examine all that.