Apple doesn't charge money for iMessage in much the same way Microsoft doesn't charge money for MS Paint. iMessage is included as part of an Apple hardware purchase. Running a messaging system that likely handles billions of messages—with photo and video attachments—every day is not free. Apple's device sales subsidize the cost Apple pays to run this system.
Beeper using this system by exploiting a technical loophole is theft in a much more direct way than pirating a copy of an audio track is, I think.