In some species, disease transmission can be a legitimate issue.
In other species, it comes down to whether the population can bear the increased harvest levels that might result from baiting. In much of Europe, fishing with bait is illegal because restricting to artificial lures is one way they keep populations at sustainable levels.
Sure, there are other ways to protect populations (shorter seasons, reduced limits, etc.), but restrictions on methods of taking has always been a part of managing populations - and restrictions on baiting are just a subset on restrictions on methods of taking.
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