But "copyright protection can extend to APIs" is all that the courts' decisions amount to so far. As the article says, the case has been remanded back to the district court, which will be trying to answer the question, "Given that APIs are not inherently unprotected, are Google's actions in this case punishable, or did they amount to fair use?"
Here's how that's gonna go:
Allsup is almost definitely going to find it fair use, and (with a little less certainty) the Federal Circuit is going to reverse that decision when Oracle appeals it. At that point, we're back to waiting to see if the Supreme Court will hear Google's arguments, but this time their argument will be that, APIs being unprotected or not, their actions were essentially no different than the ones the Supreme Court determined were defensible in Lexmark v. Static Control in pursuit of interoperability. First Amendment probably won't actually factor in to this.
This is assuming that neither Oracle nor Google capitulates before it makes it that far. Oracle probably won't. Google might.
That's not an affirmation. An affirmation would be if the Supreme Court took the case, and agreed with the Federal Court. This is "we're not going to bother", which leaves the decision as good precedent in that Federal court (but not in any other).
It is true that they implicitly affirmed the decision in this particular case, but as to the larger question of copyrightability of APIs, as I mention above, the reasoning for denial could just as easily be they didn't think this case would be a good test for that question for whatever reason.
Wikipedia cites a few cases in which the Supreme Court has explicitly stated this in [1] (see paragraph starting with "Conversely...")
This is one of the reasons why the FSF, for instance, sided with Google but still urged the Supreme Court not to take the case. They said the GPLed OpenJDK already gave Google the right to the APIs in question, but also noted that there wasn't precedent any court needed to defer to for the Supreme Court to address anyways.