I look at it like this, Hawk is the CO, he looks after his people, he's not afraid to lead them into battle, therefore he has the love and respect of his troops, but he's still the CO. Duke is the top kick, the first sergeant so he has the most "interaction" with the troops, and leads them into battle "on the ground" and they probably respect him for that, though I don't think all of them like him. Flint, Torpedo, Lt. Falcon all out rank Duke, and probably just lead teams for specific missions.
In all honestly, rank doesn't seem to mean much in the Joe verse, I've seen Scarlett order Beachhead around, when technically he out ranks her, and that is just one example, so essentially, it's more about what works for a specific writers story whether it be comic or cartoon, not about actual rank.
That's just my opinion, I could be wrong.
