Fox is actually suing DISH, not individual customers. They're not saying that if you as an individual choose to skip the commercials, then that is infringement (which this article seems to be trying to spin it as). What they're saying is that they claim the entire stream (content + commercials) is copyrighted, and DISH is only an authorized distributor for the entire stream. They want to be able to say that removing the commercials from a TV show is creating a derivative work, and DISH then distributing that derivative work is where the copyright infringement comes into play.
Personally, I think it's nonsense. However, this exact same issue has already been raised with the courts. In 2001 several TV broadcasters sued ReplayTV for having a similar automatic commercial skip function, and the broadcasters won.
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