I should think the same reason we have a Federal Bureau of Investigations on top of local police forces, the Justice Department on top of District Attorneys, standing land army on top of national guard units, etc.^ There is a Federation Naval Patrol (which is non-Starfleet) but that organization is probably more like a Coast Guard.
The idea that there's a Federation Naval Patrol seems pretty bizarre to me, though. Why would a Federation agency patrol oceans when planetary governments are probably better suited for such a task? Unless the Naval Patrol is strictly for newly-colonized and under-developed worlds that don't yet have their own navies, anyway.
Well, except that it's not like the land that the FBI operates on just stops between towns. Whereas, oceans are confined to a given planet -- it makes much more sense for that to be a planetary matter rather than to have an inter-planetary agency.