I don't think any system or process can be made flawless. Humans are imperfect, and they make mistakes. So, when I hear people say the system is designed so that only those who are proven guilty beyond a reasonable in a court of law will suffer punishment, I realize that there are holes in that idea.
But I've also seen it expressed like in the scene from The Fugitive I put up earlier, where they were saying that being proven guilty in court is akin to an absolute truth that only some madman would question. In their minds, there was absolutely no chance he could be innocent, since he was "proven guilty."