What's happening here is that Level3 and other transit providers are starting to see their industry be squeezed by the big ISPs. If you have 5 ISPs that serve 90% of the customers in the US, and 10 service providers that generate 90% of the bandwidth, why do transit providers even exist? I think they see their market share decreasing significantly as more of their customers follow in Netflix's footsteps, so they're trying to pile on and start a grass-roots outrage like Netflix did. Problem there is that most people haven't heard of Level3, so it makes it more difficult to get people behind them.
And you are completely right about the whole Netflix issue being Netflix and Level3/Cogent's problem. Level3 and Cogent have business models based on selling transit acquired through settlement-free peering. Settlement-free peering assumes that bandwidth usage is roughly symmetric: when it's not symmetric, the side sending more bandwidth has to pay. Level3's position here seems a bit hypocritical: if they had a customer that was routinely sending data at a 20:1 ratio, they would charge that customer for sending more bandwidth. But they're expecting the big ISPs not to do the same to them?