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The vast majority of Shuttle cargo (esp. post 1986) was NASA/other US government.
Thanks partially to the STS the US lost its monopoly on commercial launches for the Western world.
>it was used for three decades which tells me it was at the very least cost practical to do so.
That has been explained repeatedly by multiple people in this thread, with sources.
If you want, you can look at NASA budgets (or even just SLS procurement) to see how much the program cost them to run. The decision on which platforms to develop and use is made by Congress, which has goals (mostly job$ and contract$) other than making an efficient or effective spacecraft. Look at how delayed Commerical Crew has been to see what Congress is willing to do for new spacecraft. Or Senator Shelby's opposition to a propellant dep*t.