[semi-off-topic]Pokémon are completely sentient and in some cases even smarter than most humans (particularly psychic types with Alakazam boasting an IQ score of more than 5K). It has been alluded to that pokémon (on a general basis) are OK with trainers capturing them. It has been implied that the bond formed between a pokémon and it's trainer is what allows them to become stronger much faster than in the wild. Also many entries in the Pokédex imply the existence of normal wildlife (when they are comparing the pokémon to real-world creatures) the only difference being that the top predators are obviously pokémon. [/semi-off-topic]

On-topic: As a Brony, as much as it shames me to admit, I wouldn't love PETA if they did attack MLP, heck I can barely tolerate them and mostly because I try to avoid them as much as possible.