they are protected by Federal Law. Occasionally permits do get issued to kill nuisance seals.
Seals have been common in our local rivers for as long as I have been fishing them. I'd say river sections close to tide water are part of their natural habitat. I recall seeing seals in the lower Fraser in the 60s while bar fishing. I also saw people shoot at them. They were bad shots and the seals soon reappeared. Other than at Furry Creek I've never lost a fish to a seal locally. I have lost fish to loons while lake fishing. Once you wise up to it, it is fairly easy to avoid that.
Many fishermen seem to hate and want to harm just about anything that gets between them and the fish they seek. Seals, eagles, otters, killer whales and other 'predatory' species of fish. I believe there was once a bounty on Dolly Varden (aka Bull Trout these days) in BC. Now they are a highly desired and sought after sport fish & pretty much catch & release in BC rivers.