And I'm curious how many people finished reading that comic thinking, "Wow, what a great depiction of Superman!"
I strongly believe it is the best depiction of Superman... and Batman for that matter. Heroes can be flawed... lot more interesting when they are.
There are several instances where Superman has been depicted as the pawn of the government. This makes sense for several reasons:
It's natural that the government would want to control an individual of his abilities. Would it be better to depict Superman 30 years in his career and the government to have simply capitulated to unregulated weapon of mass destruction doing whatever it wants? Of course they'd aim to gain control over him.
Superman has always put his faith in men. He wants to be like them. He trusts the overall goodness of individuals.
Superman has commonly classified himself as an American. It's not unnatural that he'd want to serve like others do. The American Way can be a much more tricky concept than it was in the 30s.
The Boy scouts of America is one of the biggest youth organizations associated with the military, and that's what Superman is - he's a type A personality boy scout.
From a utilitarian perspective, the greatest good for the greatest number would mean limiting vigilantism, so an effort to control and limit vigilantism could be highly justified.
IMO, TDKR was easily the most complex, 3 dimensional, and natural progression for the character. Just because it doesn't fit into this "do good in all circumstances" box that people like to put Superman in, doesn't make it wrong. In fact, the key difference between Batman and Superman is Superman's willingness to put his faith in humanity versus Batman's need for vengeance against the worst of humanity. They'd naturally come into conflict, and they're disagreement over government influence is the most obvious reason why.