Strictly speaking,the courts were not given a chance to weigh in on the matter. A panel of government bureaucrats within the Library of Congress, in consultation with government lawyers, made this decision after considering briefs from interested parties on both sides of the argument.
Now, the courts have clear instructions not to consider the DMCA's anti-circumvention clauses when dealing with any potential cases that might arise surrounding a mobile phone being jailbroken (or rooted if you're talking in Android parlance, or whatever other word you'd use to describe the process in other phones...).
Apple never publicly showed any signs of actually attempting to press charges against any individuals for violating the DMCA by jailbreaking their phones, and it is entirely speculative whether or not Apple was ever actually planning to. This was a preemptive move to prevent Apple from doing so.
Now, if Apple wants to press charges (and still, there's no evidence that they are planning to), they'll have to look for some other point of law outside the scope of the DMCA anti-circumvention clause. If they managed to find such a law, and if they could successfully persuade a court to agree with Apple's reasoning, then it still might be possible for Apple to force the issue and have jailbreaking declared illegal by other means. But, again, there's no evidence to support any notion that Apple is actually pursuing such a course of action right now.