Government can be accused of censorship. Private citizens and companies cannot. I cannot be forced to publish comments on my blog for instance. I am not bound by censorship laws since I'm not a government.
Yes, the first amendment only applies to government entities (in the U.S., anyway), but censorship refers to any suppression of speech by an entity.
What Apple did was censorship, just not the type of censorship that infringes anyone's first amendment rights.