Netflix had to pay Comcast because it was losing customers I've said it before, the big wired ISPs don't have any real competition. At best, there's one other big ISP in the area. So if they decide to "tinker" with Netflix's streams, customers aren't likely to leave the ISP. After all, where are you going to go if Big ISP X is your only option?
For Netflix, however, there is competition. So if a customer experiences a lot of problems with Netflix streams, even if those problems are caused by the ISP, the customers might leave Netflix to go elsewhere. One of those "elsewhere's" being the Big ISP's own video offerings. (e.g. Cable TV.)
Therefore, a big ISP who tinkers with Netflix's streams will profit from Netflix being forced to cut a deal with them and will profit from customers who leave Netflix for the Big ISP's video offerings. Abuse of monopoly at it's finest. However, I'm sure making the Comcast monopoly even bigger will solve everything, right?