While Behe’s study is useful in summarizing how adaptive evolution has operated over the short term in bacteria and viruses in the lab, it’s far less useful in summarizing how evolution has happened over the longer term in bacteria or viruses in nature—or in eukaryotes in nature. In this sense it says nothing about whether new genes and gene functions have been important in the evolution of life. Granted, Behe doesn’t make such a sweeping statement—his paper wouldn’t have been published if he had—but there’s no doubt that his intelligent-design acolytes will use the paper in this way.
Finally, this paper gives ID advocates no reason to crow that a peer-reviewed paper supporting intelligent design has finally appeared in the scientific literature. The paper says absolutely nothing—zilch—that supports any contention of ID “theory.”