Captain America: the Winter Soldier. CA had the perfect opportunity to say that "actually, perhaps the government doesn't have the people's best interests at heart, and we are the bad guys?" but shifts immediately away by saying "actually, the cybernazis who have secretly infiltrated our government are the one who have been making all the bad decisions! We're the good guys after all!"
Presumably, they were offended by the idea that the US government might nuke New York, but once it was revealed that it was just secret Nazis doing the bad things, it was fine.
Captain America: the Winter Soldier. CA had the perfect opportunity to say that "actually, perhaps the government doesn't have the people's best interests at heart, and we are the bad guys?" but shifts immediately away by saying "actually, the cybernazis who have secretly infiltrated our government are the one who have been making all the bad decisions! We're the good guys after all!"
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The DOD did approve Winter Soldier, the one they didn't approve was the original Avengers.
https://www.cbr.com/captain-marvel-mcu-military-relationship/
Presumably, they were offended by the idea that the US government might nuke New York, but once it was revealed that it was just secret Nazis doing the bad things, it was fine.