There are a couple of problems.
Cable companies used to simply be mechanisms to get content created by other companies to users, and they did so through the TV.
As time progressed, the cable companies also began providing Internet access over the cable lines.
The cable companies also changed from simply being mechanisms for transferring the content that others have created, to owning some of those content creating companies as well.
New companies sprung up (such as Netflix) which realized that they could serve content through the internet, and serve it to more devices than just TVs.
This tends to drag on the profitability of Cable TV if people start feeling they have a better costing, reasonable alternative, so customers started dropping cable. Meanwhile, content creating companies not owned by the Cable companies were given a new outlet for distribution, not having to rely essentially on their competitors (the Cable companies) for distribution, possibly at unfair terms.
So around the time that the Netflix user base was really exploding, the Cable companies started putting caps on their Internet service, along with creating their own clones of the services provided by other websites that were now serving up content.
The problem now is that the cable companies seem to be unfairly using the arm of their company that provides internet access in order to artificially help it's Cable TV and content creation arms. By keeping the caps artificially low, they keep people from being able to use the Internet to get their content, pushing people towards their Cable TV. Now, by allowing their own sites to not count towards the cap, they are telling people that they can go back to getting content from the Internet again, but only if it's provided by them.
This is compounded by cable companies being granted local monopolies, so many people don't have a choice than to use these Companies that are trying to limit what content they can receive.
Imagine Walmart buying out USPS/UPS/FedEx. People have to go through Walmart to get anything sent to them. Now imagine Walmart saying that you are now limited to receiving 3 packages per month. This would be terrible for Amazon, a competitor in getting a good number of things to customers. This is now the equivalent of Walmart saying, "You are limited to 3 packages per month, but any packages you receive from us won't count, so order from us!". This has a chilling effect then beyond simply winding up costing customers more. A student is studying WWII. They want to read Mein Kampf. Walmart doesn't like it, so doesn't sell it. They've killed Amazon. You can't get it.
TL;DR- So the issue is that because the Cable companies are controlling several parts of the entertainment business, this is monopolistic behavior that will cost customers more and limit customer options.