http://gigaom.com/2013/06/20/verizon-that-peering-flap-about...
It's not throttling, but rather the peering points along the "best" route between Cogent and Comcast/Verizon are overloaded, resulting in lousy connections between them. Look at this traceroute hop from Comcast to Cogent I just recorded:
7 he-0-10-0-1-pe03.111eighthave.ny.ibone.comcast.net (68.86.83.94) 21.377 ms 20.379 ms 19.387 ms
8 be7922.ccr21.jfk10.atlas.cogentco.com (154.54.13.161) 67.126 ms 67.747 ms 69.083 ms
40 ms to go one short hop in, I believe, the same data center.The ISPs could just eat the cost, and let it be delivered for free. Or Netflix's CDNs could just pay the peering fee. Or Netflix could use different CDNs.
The reason the VPN works is because it sends the data over a different CDN that isn't saturated because of the dispute.
At least that is how I understand it, but I'm not an expert (or even a novice).
Edit: Wait I think I understand. I messed up peering and ISPs, right? Because the CDN connects to the internet via peering, and they're charging money (which does make sense to me), not the ISPs.
Net neutrality is about stopping the ISP from artificially decreasing available bandwidth. These kinds of things adjust the real bandwidth available.