Not the least of the differences is the enormous amount of bandwidth consumed by NetFlix as the single greatest user of internet bandwidth in the world. In a limited, over-leased, QoS driven system it makes perfect sense to throttle NetFlix in order to give other content access to the circuits.
The alternative is to upgrade the entire system in order to accommodate NetFlix but then who should be charged for that other than NetFlix? Should the ISP charge all of its customers for the added infrastructure to accommodate NetFlix customers even if all of the ISP customers aren't NetFlix subscribers? By throttling NetFlix or charging a premium it passes the cost of the increased capacity to NetFlix and NetFlix customers who are really the people who should be paying for it.