Alex Jones has the complete and total benefits of free speech - he can continue saying whatever he wants without any repercussions from the government. Apple making a decision like this isn't influencing free speech in the slightest.
Free speech is not a concept that only exists in your constitution. It's a mistake to bring up the First Amendment in these cases just as much as it is to think that Free Speech only refers to the First Amendment or repercussion from the Govt.