I used to hate the idea of permits for backpacking. After seeing trash and damaged plants on a favorite loop, I changed my mind. Rangers told me limits help protect the place. Now I think it's worth the hassle to keep areas nice.
Wait, what?! Damaged plants? I mean, I get the trash thing, that's bad enough, but who goes out of their way to hurt the plants? I saw a patch of wildflowers just totally trampled once, like people just walked right over them instead of going around. It makes me so mad, it's not that hard to be careful. Maybe you're right, if a permit system stops that, then okay.
People usually aren't trying to wreck things on purpose. They just don't think. They take a shortcut across a field for a photo or let their dog run through the brush. That casual stuff adds up. It flattens ground cover and crushes insect homes. The damage happens because people are careless, not because they're actively trying to destroy a nest.