Well, the most succinct way I can put it is because we believe the Cataclysm was humanity's punishment. That it was a direct result of how we treated pokémon. And the pokéballs of old were a core part of that. It's easy to... to think of a someone as a something when you can just put them in a small ball whenever you don't have need of them, you know.
Does it make sense why we're wary?