A quarterback can only deflate a football so much. Eventually the ball becomes completely flat. No quarterback would choose to play with a completely flat ball. So why does the NFL have to tell Tom Brady how much (or little) air can be in the football when the laws of physics already do?
Just about every recent rules change in professional football has centered around making the game more comfortable for the offense. Fans want to see big gains and points. A ball that is easier to throw and easier to catch is a great avenue to this—and an avenue that in itself is not intrusive to the integrity of the game.