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I think the problem is if you view prison as a social benefit where those who have wronged can ideally be rehabilitated and reintegrated back into society, then it's helpful to not have ex-cons loaded with debt when they already have an uphill battle to avoid reoffending. If you view prison solely as a deterrent and punishment maybe making them pay makes some sense. If, like in the US prison is a big business and source of slave labour then making people pay makes business sense but there are so many problems with that already it helps no one but evil corporations.
Gotta say while I don't agree with two tierd prison systems that can be bought into, I'm not sure I see a conceptual issue with people who've committed crimes being partly responsible for the cost of their incarnation. It just needs to be implemented in a reasonable way.