He almost certainly means that from a strictly legal standpoint, rather than as a general statement. It's somewhat common for the Supreme Court to put a disclaimer in an opinion stating that the opinion was so narrowly focused that it shouldn't be used as a precedent in other seemingly analogous cases. Presumably, this comment is more of a command to the lower courts, rather than a prediction of the future.
So, if Company X wants to start a business that is similar to, but not exactly the same as, Aereo's business, any legal challenge against Company X would still have to be upheld on its own merit. Challengers couldn't cite this Aereo decision as legally relevant.
Now, whether this ruling will have chilling effects, other than its legal precedent, is a different question.