I know this episode mainly generated controversy for having some sort of pseudo-atheistic message, but what bugs me more is just how much of a jerk Twilight was. I guess her behavior here was still to be expected, considering that at this point she had mostly lived a sheltered life in Canterlot academia and still wasn't a good friend at all. But jeez, maybe at least try to understand that not everything in your world is rational or at least explainable?
Looking back now (with the perspective of all the rest of the show and what it's set up), I suppose I'd expect ponies to generally understand that they're magical creatures in a magical world, to understand that it's just part of living in Equestria. I don't have the pitch bible on hand at the moment, but I sort of remember the idea back then being that unicorns were supposed to be pretty much the only ones with any magical ability whatsoever, so maybe it's in that mindset that Twilight was behaving here.
As for the episode itself, I've always been conflicted on it. The moral/idea behind it always struck me in an odd way, but the comedy is pretty strong throughout, so I suppose I'd put myself somewhere in the middle of the "love/hate" reaction this episode seems to produce (though I see more "hate" than "love").