Hoffman's argument is remarkably close to Plantinga's (1993) evolutionary argument against naturalism, and Plantinga himself asserted, rightly or wrongly, that "Darwin himself had worries" about the compatibility of natural selection with the ability to reach true conclusions. And of course, the notion of "percepts act[ing] as a species-specific user interface" was discussed in voluminous detail by Kant.
Just to be clear, I don't have any problems with Hoffman proposing this idea, and I don't have any problems with Shermer criticizing it. What I don't like is the suggestion that this is somehow an idea that hasn't already been discussed for centuries.
Edit: I guess I should always make sure I've eaten something before posting. This came out angrier than I intended.