Says free diver in the article, but nothing about a flag. All the comments want to crucify the boater that struck him. They say it is similar to a pedestrian struck by a car, but I've never seen a pedestrian suddenly pop up from under the pavement, nor have I heard of one struck while a few feet below it.
Divers are responsible to use a flag. Boaters are responsible to pay attention around divers, and in general to avoid obstacles on the surface. There's more information to know before considering where exactly the fault lies in this case. As a diver, though, I will always be cognizant when near an area that could have boat traffic. Free divers don't necessarily have a choice about when to surface, so they need to be extra certain of their safety.