They probably expected it to be independent when it was created and funded to be independent…
A free press is one of the core tenets of a democracy. The government supporting that was not just unremarkable, before the current regime it was expected. This is not normal. Nobody in this administration is normal, and none of then seem to actually want to live in a democratic society.
All that is true, but dependence on the Pentagon is a vulnerability anyway. Tomorrow they could impose publishing outright lies. Free press is meant to be independent, not state sponsored.
I don't disagree with your point; I'm just seeing it for what it is.