In old world there were a dozen of "tier1" providers who would all peer with each other more or less settlement free. It is conceivable that one of these providers (I think it was Cogent in this case) was offering "low rates" to take Netflix traffic and deliver that traffic to Comcast over their settlement free peering. As traffic flow between Cogent and Comcast was increasing, Comcast refused to upgrade the interconnect to accommodate the flow. Then: links get hot, traffic gets dropped, customers complain, Netflix+Cogent asks Comcast to behave, Comcast offers to unblock the pipes via direct Netflix<->Comcast peering for a "fee".
Now I don't know whether that "low rate" that Cogent was charging Netflix was lower than a "fee" that Comcast is charging. It might be that you are right and the fee overall reduced Netflix costs. What I do know however, is that Comcast is a monopoly and if unregulated, they can start extracting higher and higher rent from Netflix (or any other content provider for that sake).