I think most generally it's because naval analogues are probably the closest when you're talking about large space-based fighting vessels. The air force doesn't operate aircraft carriers, battleships, or destroyers. The navy, however, does (or did in the case of battleships). Those large sea based vessels often class quite nicely into a lot of sci-fi media for large ships.

The small ships you see are often based off of a carrier equivalent. Even when they're terrestrially based, it makes a lot of sense to streamline your military structure to have just one "space force", rather than trying to break it up into two entities like the "space navy" and "space air force", each with their own standards and logistical supply networks.