Shanks probably doesn't conquer and rule territories like Big Mom. He probably just plants his jolly roger in places that he likes so it can be a deterrent... Kinda like Garp and Fuscha Village.

But Shanks might not be viewed as scary and protective as Whitebeard was... So his Jolly Roger in a high traffic area like Fishman Island might not have been enough a deterrent. It might be why Jinbe chose Big Mom as she has a large network and tighter control over her territories, visiting them regularly (albeit to just collect payment).

So yeah... Even though it's likely Shanks might be a stronger individual than Big Mom, her network might be feared more than whatever system that is under Shanks (which is probably nothing serious but "I like you. Hang my flag and call me if you need help."