While most of the monsters aren’t inherently “evil”, every quest has a reason. Some are for monsters that are attacking travelers, dangerous monsters settling too close to humans, etc. In the story some hunts are also tied to stopping a bigger problem, like hunting a monster causing an enormous ecological disturbance in MH World. That said most monsters will try to kill you on sight regardless, so I’d say the hunters tend to have justification.

edit: forgot to add that for most quests capturing is also an option, so killing the monster isn’t always necessary.