There's are several answers to your question.

1) To a certain extent it does apply to every case the Court doesn't hear. Although such denials of cert aren't supposed to mean anything you will nonetheless see in briefs something like:

"The Ninth Circuit held blah blah blah. Doe v. Smith 108 F.3d 1147 (9th Cir. 2012), cert. denied, 112 S. Ct. 60 (2013)."

The intention is to imply that a majority of the Supreme Court at least didn't strongly disagree with the Ninth Circuit.

2) Most cases come up to the Supreme Court from the Court of Appeals, not a special three District Court judge panel. The uses and limits of CoA judgement in their own circuits and in other circuits are well understood because it happens so much. That's not the case for these kind of judgments.

3) The nature of the decision itself is unusual. Most cases are fact bound, even most cases that are dealing with precedent work around the edges of existing cases.

The precedent the court below was dealing with -- Vieth v. Jubelirer -- is really unusual. In it four judges would have held that partisan gerrymandering cases are always non-judiciable (i.e. courts shouldn't hear them) four would have held that the such cases are judiciable. Justice Kennedy wrote a solo concurrence that represented the decisive vote. In it he wrote that such cases were as of then non-judiciable because there were no judicially manageable standards that could be applied. But he left the door open for such standards to appear in the future.

The court panel below held that the standard proposed by the plaintiffs was the standard that Justice Kennedy had been looking for all along. Leaving that in place without comment would have looked more endorsement than usual.