Stephenson really should have been called out in the article on the assertion that every megabyte downloaded has a marginal cost. There's no way to squint at that hard enough to make it true.
The article you link to really doesn't support your claim. Yes, bandwidth is plentiful off-hours and expensive during peak times, so pricing based off of total usage regardless of when the data is used is crude. (This is why voice plans have had things like "weekend minutes".) But a heavy user really does have a higher marginal cost than a light user. In the absence of more complicated pricing (which consumers often reject), data caps are reasonable.
I'd love to be able to pay reasonable data charges per megabyte. The problem is that overages are currently insane, compared to what it costs for fixed monthly rates.
Maybe he phrased it badly, but his point still stands.
More users downloading more stuff requires more infrastructure.
At some point enough users downloading enough stuff will saturate the hardware, and they'll have to throttle usage, or spend a boatload on new infrastructure.