See discussion above. It's all about the retransmission fees that the networks are getting from the cable companies. Aereo is breaking that model.
The networks are the ones making extra revenue by forcing the cable companies to pay them to carry shows on their systems. The historical reasons for this are complex but I would refer you to a nice NPR podcast that explains it better:
http://www.npr.org/blogs/money/2013/09/27/226891181/episode-...
So back to the problem at hand: Aereo has found a way to skip around those carriage fees that the networks demand. The courts have backed them up. So the real problem is that the cable companies are now asking "why should we pay if Aereo is not?"
It's not a cable-vs-OTA war, it's the networks-vs-everyone-else.