Fury hid a lot of stuff from Steve, because the latter did not have the authority to know everything that the former did. Fury was the Director of SHIELD, a spymaster and Steve's boss. There is no need to create some excuse on why Fury never told Steve everything. Fury treated Steve to information on a need to know basis, just as he had treated his other agents. The problem with Steve was that he thought he had the right to know everything that Fury did. And he had expected Fury not to keep any secrets. Which revealed not only his naivety, but also his arrogance.
It's not that Steve thought he had a right to know everything Fury did. That's bonkers. It's that Steve thought he could better protect the lives of everyone involved in the mission if he'd known the whole story. Fun fact, he's right. That doesn't make what Fury did wrong, however. Fury has reasons, he has schemes, he has secrets. Steve doesn't work that way. Steve and SHIELD are incompatible, which is thematically critical to the movie. Steve is about teamwork, about the greater whole doing good work to keep people safe. He fundamentally wants to be part of a team built on trust and aimed at helping people. He joins SHIELD because it's the closest he thinks he can get to that.
He's wrong. Which is great for the average joes of the MCU, because Steve being incompatible with SHIELD saves the entire world. SHIELD is literally a shadowy cabal of secrets within secrets hiding behind other people's secrets, and with it's own agenda outside it's official mandate. If nobody questions, HYDRA wins. If good people do nothing when they see something awry, evil prospers. People have an obligation to speak up when they see things that are wrong, even to voices of power and authority. Steve is that voice in Winter Soldier.
I think you're coming at this from an interesting standpoint, assuming that no junior officer or employee has the right, or even the moral necessity to confront their boss/employer/commander when the situation calls for it. That isn't how the world works. Yes, Fury could absolutely have punished Steve for the outburst. He could have fired him, demoted him, or probably any other number of punishments. Steve gets off the hook because of his fame, his legend, and the fact that yes, at that moment, Fury knows Steve is right. If it was about protecting people, Steve is 100% correct. Of course, the mission had nothing to do with protecting people, and that's what Steve has figured out and is pissed about. It's the fundamental, nuts and bolts incompatibility between the man Steve Rogers is, and what SHIELD is. (Even setting aside that SHIELD is merely a HYDRA front.)
Speaking frankly, if this scene is a display of arrogance, I hope there are a lot of arrogant people out there. Speaking out, challenging authority when it crosses the lines, these things are difficult, and frequently dangerous. But necessary and good.