I'll bite.
Suing the fishermen is heavy handed, but these colonial land grant/riparian rights situations are common. Our bay and beaches here belong to local towns under a colonial era patent, basically a land grant from the King that predates the US. It's held up in court many times. It can work in our favor, as it has been used to blunt heavy handed state and federal regulation. For example when NY State tried to implement the idiotic salt water fishing license, the towns here sued to block it since they are charged with regulating fishing in these waters and they didn't wish to require licenses. They won a few rounds, before all that got scrapped.
Everything is owned by someone, whether an individual or "the people" i.e. various collections of them.
I agree it's weird that a river would suddenly be private at a point along it's length, but where's the cutoff on that? If you have a muddy ditch of a brook 2 feet wide running through your back yard, you want some guy in waders walking through while you're having a barbecue, just because further on it's a navigable waterway? If you put up chicken wire at either end and put some Koi in there, are they your fish because they are on your property? Apparently the law (or some law, some places) says they are, so someone else is not free to catch them.
The guy paid money for something in a deed, he's entitled to have his day in court and determine what he actually does own.
I believe this also came up with some of the midwest flooding a few years back - guys were fishing where water now was that was actually some guy's farm field. He didn't lose his land rights because some water temporarily washed over it.