Agents of SHIELD did complicate this in earlier seasons, by having some good guys locked up and the prisons infiltrated by HYDRA, and the lock-down program shown as wrong and inhumane for several characters. But they quickly threw that out the window!

Weirdly, DC Comics has a ton of supervillain prisons which definitely have due process for getting put in there - Belle Reve from the Suicide Squad being the most well-known - and only secretly get weird, whereas Marvel Comics has things like Ant-Man shrinking down supervillains and imprisoning them in a tiny prison, or Reed Richards running an inescapable prison in the Negative Zone, as well as some more normal supervillain prisons like the Raft (part of a regular prison). But the TV shows and movies reverse this!