If you're walking or flying, and come across a ban line, you can adjust your position accordingly to avoid it. However, if you're boating, depending on the size of your craft, the person steering the boat and the passengers may be separated by some space, resulting in passengers abruptly being plucked out of the craft and booted when crossing a particularly harsh ban line that the pilot of the boat did not see. As you can well imagine, such a scenario completely destroys what had until then been a pleasant outing.
This doesn't even take into account the difficulties in maneouvering a craft, versus moving oneself.
It would be nice if there was an alway-visible demarkation of ban lines that crossed open waterways, kind of like how strings of floating bouys tell boaters to keep away from certain segments of the shoreline because there may be someone swimming there. They would be relatively unobtrusive, and not spoil anyone's view (unlike ban lines), yet still allow people attempting to navigate a craft to locate the public use areas of the waterway.
Alternatively, the public use areas of the waterway could be lined with bouys, so that boaters would know it was safe to stay within those boundaries. If they knew the area, they could cross the line, but people unfamiliar with the region would still be able to use the public areas.