Most, if not all of the "junk mail" you would be getting will not unsubscribe you by simply hitting 'reply' and putting "REMOVE" in the subject or body of the email.
Companies will often put a fake email address in the "reply to" portion of the email. This is usually done in the mass-mailing application.
There are several reasons for this. One of which is that companies like to send out mass-mailing in a phase approach. Sending say 1000 emails at a time.
If in that thousand emails fifty have bad addresses, then the account responsible for sending will start excepting "no such address" bounce-back messages.
So as the mass mail progresses more and more bounce backs would prevent the mailing from going as smoothly as possible.
More often then not these companies provide an alternate link at the bottom for unsubscription requests.
Still other companies or individuals simply don't want to make it easy for you to unsubscribe. The link they offer often doesn't work or even worse signs you up for even MORE spam mail.
Apple has assumed, correctly I think, that the best solution is to minimize the impact this 'junk mail' has on your email experience. By automatically routing the mail to a junk folder, you can rest assured that your wanted mail won't be deleted by the program AND that the unwanted mail will not be allowed to populate your regular inbox.
I hope this helps with understanding what the thought process is on 'junk mail'.