Are you forgetting one key Constitutional concept: Innocent until proven guilty. It's the cornerstone of our legal system. During these early appearances, the suspect is just that: a suspect. They might be guilty. They might be completely innocent. We don't know. The judge doesn't know. The cops don't know. Lots of suspects get released on bail because they are only a suspect. Those who can't afford bail shouldn't be chained up like animals.

After a felony conviction, I have no issue with it. At that point, the Constitution is also clear that the government can punish the guilty. Shackles during transport of convicted felons makes good sense to me.