The rank structure in the new BSG is based on that from the classic, which was a result of Glen Larson knowing nothing about military, indeed he purposely arranged the ranks in the order of Captain, Colonel, Commander because that was how they went alphabetically. For the new series, Ron Moore considered going with a more realistic naval rank structure, but decided to go with the classic series rank structure for nostalgia sake.
I've sometimes wondered if BSG "Commanders" might actually have been Commodores (Originally thought of it re: Commander Shore of the World Aquanaut Security Patrol (a specialist patrol/strike group of the World Navy) who outranked Captain Tempest, skipper of the eponymous Stingray.)