Simulation hypothesis has at least one problem in common with Boltzmann brains, as the evidence that leads to that conclusion also says you can't trust your reasoning process including that you have reached this conclusion.
The reason why you can't trust your reasoning process is different in each case, for Boltzmann brains it's that your entire history is as much a dice roll as anything else and therefore most likely just random noise.
With the simulation hypothesis, the you can't trust your reasoning process is that for any finite simulator, it's always going to be easier to simulate something simpler than reality, which again means it's always going to be wrong about something in that reality. If you posit we are more likely to be simulated beings than physical, it's much more likely that we're a lazy simulation than a high quality one, and a lazy simulation… well, something something stochastic parrot. (We don't know what qualia even is yet, and I've only heard one reasonable seeming idea for even testing it, so for all we know stochastic parrots are as capable of qualia as we are).
The Simulation hypothesis is a rational extrapolation of possible things. Quite different than religion.