He never directly states that they are being charged based on revenue, just that what Apple is trying to charge works out to 15-30% of their revenue. It's sort of splitting hairs, but something that is pretty much a problem with any business that relies on larger businesses. For instance a small Architecture firms pay a much larger portion of the their revenue each year for software license than larger firms that use the exact same software but can better utilize their licenses and be eligible to receive volume discounts or other perks.
The Apple Store, not that it's uniquely Apple, are notoriously harsh on startups since the percent they take for distribution is often larger the smaller the business is. There are some business for this, like a customer that brings in $10,000 may have as much or more overhead than one that brings in $1,000,000 so it makes sense for Apple to incentivize large customers. To that smaller customer any such reason it pretty well mute though, it's making it harder for them to keep the lights on.
Not trying to excuse Apple with some of their practices, they have proven repeatedly that their business practices are shady at best, just not can't really say they are singling this guy out any more than anyone else.