Think of it from the Instructors point of view, they have X amount of people learning to drive, now if they are learning in a manual car, it would be more expensive for the instructor to replace a gearbox rather than brakes. As if the students are down shifting, they may select the wrong gear/crunch the gears etc, which adds extra wear and tear on the syncro's and gears, which means the gearbox may need changing sooner then normally needed, so in that case yes replacing brakes is cheaper.
Not all instructors use autos, I first started out in a Manual Car when I was taking classes...I then changed to auto, as I was crap at the slow speed maneuvers, and the parents wouldn't let me practice in the 1 manual car we had. Of course, things may have changed now, I don't entirely know, I know last year or so, my mate was learning to drive in a Manual Car.
Why is the focus all on the young people? I see plenty of middle aged people and older people in accidents or causing them...hell, I almost got T-Boned today on my way back from Victor Harbor by some fuddy-duddy not watching what they were doing.