Even if we are in a simulation, it doesn't mean that human life or even just life in general is the goal or subject of the simulation. I haven't seen any of the people who speculate about this make any sort of claim to the contrary. I mean we could just be a minor side effect. After all why would you simulate... or create... a universe as big, old, and complex as the one we live in if all you were concerned about was a single short-lived species on a tiny world.
You are assuming the simulation is as big, old and complex as we believe it is. Games use procedural generation to create universes and planets, the universes that we perceive to be "big" could just be that.
History and any science to prove history could all just be input or rigged data in the simulation. We would never know, the simulation could have started yesterday. You are right we could be a factor in a simulation and not the actual subject... again almost impossible to tell.