They are willing to do this because the transit providers can not handle their traffic efficiently. So why is Netflix complaining?
If you were an ISP would you provide free transit to everyone? If you did, you would be out of business.
ISPs are being paid for transit to their end users _by their end users_.
(The relevant quote is: "(1) [Transit Networks (e.g. Cogent)] carry traffic over long distances and (2) they provide access to every network on the global Internet. When Netflix connects directly to the Comcast network, Comcast is not providing either of the services typically provided by transit networks.")
Netflix is questioning the premise of your question by suggesting that Cogent and Comcast are _not_ providing the same service. I find the argument fairly compelling, though I'd be willing to hear counter-arguments.
So, if the existing backbone transit providers are not adequate, Netflix should be and needs to be covering the cost of the bandwidth when directly peered with Comcast. Otherwise the cost of this bandwidth is transferred to Comcast customers, all of which do not use the Netflix service.
It really comes down to this... Do all Comcast subscribers deserve to pay for bandwidth that is created by the minority that uses the Netflix service? I do not believe so. The cost should be with the Netflix, they create the overhead, they should pay for it.
There's no clear answer because there's a lot of competing and overlapping incentives here. But at the end of the day, if comcast has to foot the bill to improve quality for netflix customers, how is that fair to comcast customers that aren't using netflix? It is pretty sensible to think that Netflix users should be paying for Netflix service. If Netflix is selling me streaming video without also having a suitable CDN to get me that video, I suggest to you that they've sold me something they can't deliver on. If nobody can build that CDN because my ISP sucks and makes unreasonable terms, netflix should probably stop selling to users of my ISP.
This really reminds me of everyone who was complaining about UPS around the holidays for not delivering their amazon packages in time, even though UPS wasn't giving any shipping guarantees due to the peak demand. Amazon was still providing estimated arrival dates, however, but it turns out those weren't based on much (or at least, enough).