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Basically it is so that each branch can organize it's own set of forces for it's own missions, whatever those happen to be.
We could simply have a "military" and have all weapons and personnel under the same command structure, but it would be very hard to be efficient, and certain kinds of missions need certain kinds of people, skills and experience.
Naval pilots are particularly skilled in Naval operations, and the command structure is much more simple if the Navy commanders can command their own pilots during their own missions, without having to link up with another branch, eg the Air Force.
This is also why the Marines have their own Aircraft. That way they can talk to their own people that are speciallized in dealing with supporting the marine ground units.
It's just a more efficient way to set things up.
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