I think you maybe missing the point slightly...
Taking your shops stocking a magazine argument a little bit closer to the truth, would be:
A shop stocks a magazine and charges the publisher 40-70% for each magazine it sells. I buy the magazine and like it so much I decide I want a years subscription to it. Now I fill in a form in the magazine and send it to the publisher along with payment which is generally in the region of (price x 12) - 40% (that they don't have to pay the newsagent) and I get the magazine through my door once a month until the year is up and I pay the vastly reduced price again for a subscription.
What Apple are trying to do here is say that the form you fill in and send to the publisher should instead be sent to them for no apparent reason other than you bought it through them, which I might add is the only place to buy such things so I call it by it's proper name a "Monopoly". So it's quite clear to everyone that Apple are blatantly abusing their monopoly to demand publishers use a system that gives Apple a 30% cut for having sold you 1 magazine at some point.
Now publishers who want to sell through the app store will have to either absorb the 30%, possible but unlikely, or they'll pass it on at least in part to you and me the customer. Apple won't missing out on their cut, the Publisher can't miss out and reduce it's margins so I'm left paying extra for something Steve Jobs hand no hand in!