Tony accuses Natasha of not being able to let go of being a double agent. In fact, it’s Tony who isn’t able to let go, in this case, of the idea that he’s running this show. He’s too used to having his words and ideas deferred to for him to understand that, this time, no one’s listening to him. Even when he’s confronted with that in the next scene on the prison ship, he can’t internalize it. Instead, he vows to play petty games with his phone the next time the Secretary wants something from him.
Natasha, however, knows she’s not running the show. She knows the people making decisions aren’t listening to her and haven’t been since she was a child. Her trainers didn’t listen to her. She listened to them or she died. The same was true for her handlers. Forget politicians. Death may not be overtly on the table, but listening-wise, they’re no different. The only people who ever listened to her were Avengers, which is why she’s an Avenger. Right now, though, most of the Avengers have too much going on to be able to really listen to each other.
When no one listens, it doesn’t matter what she says. What matters is surviving long enough to get out and do what she needs to do. So that’s what she does. That’s what Wanda does. That’s what Sharon does. They comply until they defy. They save their breaths and their resources until they need them.