1) Simple_Min: quantum mechanics does not preclude free will - in fact, it suggests that there *must* be free will. After all, even God cannot bypass quantum mechanics' probabilistic nature, and thus cannot predict/guide our actions.
2) About processing power: during a university course on computer theory, I think I heard the teacher say that the theoretical maximum of calculations a second is about 10 ^ 50th, given minimum distances (between memory locations) of one electron. Quantum computers could easily solve that upper bound.
3) The writer assumes some advanced civ would build many computers (logical), but then assumes they'll run many simulations, as the required computing power is small. Question is: why the hell would they run his "ancestor simulations" so many times? One would assume they have better things to do. But perhaps it's part of their history lesson: a simulation of human life from beginning to current days (future for us), all compressed; we wouldn't know we're compressed, of course.
4) if *we* are in a simulation, wouldn't our simulators be in a simulator too, logically speaking? In fact, according to his logic, practically everyone should be in a simulation, again leading to the question: why? (And to the simulators: who?) The writer addresses this problem by stating that our simulators will likely be simulations too. Nice, but probability doesn't work that way. If it did, one could argue that *everyone* is in fact a simulation - after all, the odds of anyone being real is negligible...
5) Does all of this really matter? As with the older theories about reality being some sort of dream or something, the answer is obvious: no! One has to act as if the simulation is real, in order to survive in the simulation.
6) Finally, the writer brings in religion, and states simulators *in* simulations (er...) will have to assume there's an afterlife, and they'd be punished for being bad to *their* simulations. This cannot reasonably be true: a simulation will not have an afterlife at all, because a) the survival of simulated humans would ruin future simulations, and b) a simulated afterlife is irrelevant to the simulation. Also, simulated evil, why punish that? It's part of the simulation, after all!
7) Finally, my original comment still stands: advanced civs with the capability to run such simulations do not mean we are likely to *be* simulations. That's only true if you accept that the number of simulated humans is way higher than the number of real humans. Which then leads to the obvious question: "what *is* real", from Matrix 1...