My recollection of the government authorized accounting for the STS was so disconnected from actual costs and cash flow it would have made Enron blush. It was based first on the marginal procurements and expenditures for each flight, including labor. The infrastructure to support space launch capability (mostly labor IIRC) was not fully accounted for and the broader overhead of NASA, like security, was entirely left out of the program budget. Even if supporting the JSC or KSC was the primary reason for the overhead.
For those who don't remember how brazen Enron was, they engineered a way to book profits off the increase in the price of their own stock while insulating the income statement from share price declines.
This seems quite reasonable to me if you are comparing the STS with other launch systems. Fully accounting this seems a but like budgeting the cost of maintaining your driveway, garage, and burglar alarm as part of the cost of running your car!!
You can't say,
"it costs X dollars in infrastructure and manpower to run the the STS Lauch System, so if we switch to the XYZ Launch System we can save all that money", because the XYZ Launch System will still involve infrastructure and manpower costs. The question that really needs asking is, will STS' replacement, SLS be cheaper to run and give you a bigger bang for your buck, and if so will the cheaper costs be enough to offset the initial, research, development and infrastructure set-up costs over the lifetime of the SLS.
On another issue, the cancelling of the STS program has sounded the death knell for the most successful science spacecraft ever launched, the Hubble Space Telescope. Without STS to run repair, maintenance and upgrade missions, HST will probably fail, and I don't believe SLS will be up and running in time to save it.