I suspect that this is the same resistance to a third party pushing content that nearly every IP owner has shown over the years. It has nothing to do with being compensated. It is likely easy to grab viewer metrics from Aereo and renegotiate the value of those viewer impressions with advertisers. I'm guessing that Fox just wants that control - they want to roll their own service, the same way that all of the music publishers wanted to roll their own streaming/subscription service, the same way that the cable companies want to roll their own VoD service, and the same way that the film studios want to roll their own VoD service.
It's no secret that these groups have all failed. The music industry tried and failed over and over again, with Apple dominating that marketspace now (and the IP owners are still managing to be compensated for this). The cable companies and film studios have also failed to run their own VoD services that are competitive with Netflix, yet they are all compensated for their IP streaming. This is just the same repeat behavior.
I'm no expert, but it would seem to me that content producers might want to stick to their core competencies, and excellence in broadcasting (or lack thereof) is showing to be unequal to excellence in developing a digital distribution model. They've failed over and over, while the third parties have succeeded almost exclusively...and in spite of lack of cooperation from "legacy" media. I know that the legacy IP owners want to maximize their profits and control by running their own digital distribution networks, but this seems akin to having their cake and eating it too - and it has proven to be historically risky.