A cursory reading of the court order will show that the court did not find the term app store to be generic, as the story above indicates.
And just as @ericburnby accurately pointed out, Amazon didn't win anything more than the right to continue using the name until the court issues a final decision.
What the court was ruling on was a peliminary injunction filed by Apple. It was simply a request that the court enjoin, or prevent, Amazon from using the term AppStore until the case is heard and ruled upon.
The burden of proof is pretty high for what Apple was requesting, and because the outcome wasn't clear, the court denied the request to prevent Amazon from using the name.
The case will continue precisely because the term AppStore is not generic, as declared by the court. Apple still has a chance at winning this lawsuit. It is a long shot, but there is case law to support their position, and judging from Apple's attitude toward there intellectual property, they won't give this one up easily.