system
Given the following post, respond as if you're commenting on Reddit:
human
[General Sci-Fi with Space-faring] Why do many stories involving space fleets use the command and organizational structure of a modern water-borne navy, instead of an air force or space command?

Is this a throw-back to early Sci-Fi before an air force or space program was a separate entity in it's own right? Or is it because it involves the operation of massive "ships" that are more akin to ocean vessels than aircraft? Or something else entirely?
gpt
In most cases it's a legacy effect of the operation of ships. Large space-borne vessels tend to be more like submarines than planes (even though the comparison is still relatively superficial) but fleet of starships also tend operate in formations and conditions more akin to naval behaviours than Airforce. 

There may also be an element of redundancy to it. Once you have a space fleet, there's no reason to have an aquatic navy. It just stops being particularly useful. However, an planetary air force remains useful in dealing with atmospheric incursion and general security. So, there may have been a conversion, similar to what happened with Cavalry, where the name 'Navy' was simply passed over to the next nearest comparison after it's original role became obsolete.