Secondly, think of technology. That's why humans are the dominant species now after all: we create tools to make us more powerful than the other species. In the world of Pokemon, the primary tool we use is the PokeBall. We use it to capture the Pokemon at which point they are at our mercy to some extent. But even if you're not like the Rockets and therefore don't rule over Pokemon with fear, healing technology in the Pokemon Centers keeps Pokemon healthy. They could not remain healthy without the Pokemon Centers, which were created by humans.
Besides, if you go by the anime, many pokemon enjoy fighting and those who don't participate in contests and whatnot. Worker Pokemon work alongside humans. So in actuality, according to the anime, Pokemon all have the choice to do what they want and they WANT to help humans in most cases. There are some rogue Pokemon that hate humans, but not the majority of them.
Also think about cases where the Pokemon knows how powerful they are and how weak their trainers are. Charizard didn't listen to Ash. Lucario didn't listen to that one gym leader. Etc etc. But over time they grow to respect their trainers.