Here's my quick take:
1) The court was right that the allegations of a horizontal conspiracy (between competitors) is too flimsy. Even though the court is required to treat factual allegations as true on a motion to dismiss, Run Gum was required to plead enough specific facts to make their claims plausible. This happens a lot in antitrust: Plaintiffs want to plead horizontal conspiracies because they are usually per se illegal, and there's no need to get into balancing of pro and anticompetitive effects. But usually a plaintiff will not have any clear proof of a horizontal conspiracy--just a hunch. It's tough to survive a motion to dismiss without more.
2) The court's was right in highlighting some problems with Run Gum's market definition. Restraints are only unlawful when they restrict competition in a relevant market. Markets are defined by considering the ability of a participant to raise prices in the market without buyers taking their business elsewhere (cross-elasticity of demand). Plaintiffs always want to define markets very narrowly. For example, a retailer might argue that a particular mall constitutes a relevant market, but in reality, buyers are willing to shop wherever they have to to get the best deal. (One of my favorite silly market definitions was "Bar mitzvah tours of Israel." See more at:
http://caselaw.findlaw.com/us-7th-circuit/1301571.html#sthash.Sbkft73W.dpuf
). The problem here is that the plaintiff is Run Gum instead of the athlete. From a sponsor's perspective, the advertising market is huge, and it's implausible to suggest athletes' uniforms is really a single market for antitrust purposes. (If the cost of advertising on uniforms goes up, sponsors allocate their dollars to other advertising avenues.) On the other hand, if the athletes were the plaintiffs, they would have a much stronger argument because they have no other options.
3) The court's conclusion regarding implied antitrust immunity under the Amateur Sports Act is suspect. In a normal vertical restraint case, the plaintiff has to show an anticompetitive effect in the relevant market, then the burden shifts to the defendant to show that there are pro-competitive justifications for the restriction that outweigh the anticompetitive effects. What the court did here was take flimsy procompetitive justifications as sufficient to demonstrate antitrust immunity under the ASA. These flimsy justifications would probably not be sufficient to prevail if the court were forced to balance them against anticompetitive effects, but the court has effectively made them the entire issue. I think there's a very good chance that it won't survive on appeal. (In the 9th Circuit, an appeal can take a very long time.)
4) More a comment on the lawsuit than the opinion, but Run Gum's theory seems a little strange to me. It's not entirely clear what USATF is gaining. It's helpful to have a clear story about why the defendants expected to benefit by suppressing competition. (To be fair, I have not read all of the filings in this case.)