The big ones back-haul to a major hub and then enter in to several peering agreements. Depending on what service/site you use the "best" path will be over one of those peers.
However, this means that there is usually a middle-man-network in between you and the service you want and neither you, your ISP, nor the service can directly control the quality or speed of that network. If Netflix, Hulu and Google all end up with a "best" path on a single peer its going to be bad during prime time even though other services connected on other peers may operate normally.
One version of a "fast lane" (like the one that Comcast and Netflix negotiated) is to remove that middle man and directly peer with the service. This is only available to large services because they need a presence in these major hubs as it usually requires a direct physical connection between edge routers.
Now, no matter how congested their peers get, the "fast lane" service is working well. They have probably also agreed not to charge the actual "market" rate on that link's bandwidth as it is mutually beneficial and the ISP should pass those savings to its users by not counting the service against any data caps etc.
From the outside, this looks like extortion. The reality though is that both sides pursue these kinds of deals all the time because it benefits their customers and therefore their bottom-lines. ISPs push harder for them because services, like Netflix, are incentivized to find the lowest cost transport peer which is usually not the highest quality. When that peering link is bad, customers blame the ISPs not Netflix.
Netflix used to brag about how cheap and cut-rate their cost per gigabyte was. How do you think they got such a good deal? It wasn't by purchasing the best connection to their customers. It was become some sales exec at a tier 1/2 internet transport provider oversold their poor service. We should be just as upset with the overselling of transport over peers as we are about ISPs throttling but, most of the internet citizens don't understand how that works.
Another note, most of the times when people use VPNs to "prove" that their ISP is throttling network capacity for a service, they are simply routing over a different peer (the one that connects to their VPN). In ideal circumstances this is traveling over a sub-optimal path and should suffer a little bit. However, in times of heavy congestion it is like being routed around a traffic jam. It is "very hard" with current routing protocols on the backbone to do this kind of "flow around" for congested paths in real-time for everyone. Single users are manually implementing it by hitting VPNs.