Please note in advance: I'm not trying to defend this, just understand it.
From the cited article:
The U.S. Marshals are the primary agency for fugitive operations, so at some (horrible) level it makes sense that they would see everyone in their custody as a captured fugitive and treat them accordingly.
Again, I deplore the situation described in the article, and consider it a cowardly cop out to describe routinely shackling juveniles as "for their safety."