Tl;dr: The plaintiffs/petitioners presented only a tenuous case that their records were actually collected, which reduced their perceived likelihood of success on the ultimate merits of the case enough that they were not entitled to a preliminary injunction.

Let's unpack that a little bit. This is not a final ruling on the merits of the case, and it does not have anything (directly) to do with the 4th Amendment. Plaintiffs had moved for a preliminary injunction before the district court that would have stopped the program well before the ultimate outcome of the case. For obvious reasons, the standard for evaluating such requests is high. One of several factors used for evaluating such a motion is likelihood of ultimate success of the merits.

In order for plaintiffs to ultimately succeed, they have to convince the court that they have actually suffered an injury by having their own call records collected. They need to have been injured in order for the court ultimately to have jurisdiction. At this point, the DC Circuit concluded that they do not have any specific evidence of this (and, in fact, some of the indirect evidence weighs against them). So, the DC Circuit concluded that they were not so likely to ultimately succeed that it should give them the injunction they wanted before the ultimate outcome of the case.

This is not a good sign for a plaintiffs' case, but its important to emphasize that this is an early look at it with, necessarily, the benefit of only a small amount of evidence. The case will continue in the district court which will, among other things, try to determine whether the plaintiffs were actually injured.

Of course, the predictable outcome of that inquiry is that the NSA will invoke various legal privileges against disclosing the evidence necessary to actually make a determination, ultimately rendering plaintiffs' case impossible to maintain.