Lest your comment cause any confusion, it should be made clear that the court denied their request for a /preliminary/ injunction (which seems to be very common, but you request it anyway); but, as far as I understand the situation, the judge agreed to hear the case and, after all arguments are weighed, Amazon could still well lose.

The idea is that the case does not seem obvious enough and important enough to stop Amazon from using the term /before/ Apple wins the lawsuit (which is what would make this a "preliminary" injunction), but the judge actually went ahead and claimed that Apple seemed to have at least some merit to their argument.

>So why are they after the small people like GetJar??

To be consistent. They're not out to get Amazon. They're out to own the term "App Store" and are proving it by going after anyone who tries to use it. So in court they can say that it isn't just the big guys that are infringing but also smaller players.