I guess it matters how much the physical publishing and distribution costs contribute to the cover price. If I had to guess I would say its probably not that much, if any, after considering advertising revenue. So if the majority of that cover price represents the creative and editorial costs of producing the comic then I think his argument could be valid. I think there are a lot of nuanced aspects and costs that come with the field of digital media that might not be apparent at first glance (I'm reminded of the TV writers strike a couple years ago, which was mostly about negotiating royalties from digital services such as iTunes and Hulu).
I guess I'm playing devil's advocate but without the numbers in front of me it's tough to make an argument either way.
JQ said in numerous interviews that the $3.99 cover price was a reflection of manufacturing costs.
Certainly there are other costs but that was his go to excuse when it was brought up while he was EiC.