The first amendment protects against Congress specifically. But you as a human have the right to free speech, and that right needs to be protected against private individuals/ corporations as well. If McDonalds blew up your house, you would sue for property damages instead of shrugging and saying "well it wasn't the government, so I guess they didn't violate my property rights after all."

Whether what Apple did here is actually a violation of one's right to free speech is a pretty tenuous argument. But that is the argument you should be responding to.