The ranks and protocol just make for standardized things across the fleet so people don’t need 500 different ways of doing things, and can integrate with each other more easily. Ranks make chain of command clear in stressful situations.

It's also just how real life ships have worked for hundreds, if not thousands of years. Ships are inherently dangerous, you can't discuss everything to death or have two parts of the crew follow mutually exclusive plans when you're supposed to respond to an emergency.