One of the reasons for differences is that the terrain is different in different places. If you dive Cozumel, for example, the towering coral/sponge features would be destroyed by the lines attached to dive flags, so it is not done there. In South Florida, in comparison, most of the reefs are small enough that you swim on top of them or next to them, with little chance that the line will run into anything and become entangled.
In Bonaire, the diving is primarily steep but sloping walls, and, once again, with the currents and all, there is a good chance a line leading from depth to a surface float could become entangled.
Different places also have different rules. Here in Colorado the reservoirs in which diving is allowed generally require dive flags, and you can draw a hefty fine without one.