Starfleet is a fictional organization from the fictional future. It's not the US Navy (or even a fictional version of the US Navy), so it's not "wrong" if they do things differently. That's like an American watching a show about the navy of another country and complaining that the differences are inaccuracies. They're not inaccuracies, they're differences.
For example, some countries pronounce Lieutenant "loo-tenant" and some pronounce it "leff-tenant." One isn't "right" and the other isn't "wrong", they're just different.
Because it's so much cooler that way.
Fair enough. I don't agree, but that's a valid opinion. But it doesn't mean the writers had it wrong, because they're not trying to create an accurate representation of the US Navy.
Even so, a lot changes in a few hundred years. Things once considered proper and necessary are now considered unnecessary or even improper. It's not unrealistic for future military/paramilitary organizations to do things differently than those in the present.
Calling someone "Mister" is just wrong.