I’m not totally sure I understand what you’re asking, but I’ll give this a shot – I’m taking this to mean “why don’t Pokémon rebel against trainers who do bad things?”; is that about right?
I don’t think Pokémon are like most animals – their comprehension of language and abstract concepts seems quite advanced. Most of them clearly aren’t of human intelligence, but it seems like we’re looking at something much more like a dolphin or a great ape than a lizard or a pigeon, even concerning the… shall we say ‘less gifted’ species of Pokémon out there. Ash’s Pikachu, at any rate, clearly has at least some degree of understanding of human morality, and the other main human characters’ Pokémon in the anime generally do seem to ‘get it.’ On the other hand most species aren’t concerned with that sort of thing at all in the wild. They’re perfectly capable of understanding conventional morality, right and wrong, and so on, but it’s just not something they care about unless they’ve specifically been taught to, because their wild communities don’t function in the same way as human societies do. I suppose what I’m getting at is that saying “they don’t know any better” is one way you could put it, but I don’t think it really gives them enough credit.
You could take a look at these two articles if you want more on the subject: