I understand the accounting principal where they have to charge for major updates but why does this not apply to AppleTV?
iPhone's updates are free because its users pay a regular fee that Apple gets a cut from
You don't understand, then.
Users paying a "regular fee" has nothing to do with why iPhone updates are free.
Subscription accounting has
absolutely nothing to do with the customer. The principle in play has to do with "deliverables" (in this case, the products) and accounting for costs subsequent to the completed sale. You're confusing two completely separate concepts.
Both the iPhone and the AppleTV recognize revenue on a deferred periodic basis (hence
subscription), thus allowing significant functional changes. Apple, together with several other companies, arranged for a modification to the subscription accounting rules so that they would no longer have to defer the revenue recognition, and could set aside a portion of the price for subscription accounting, essentially creating a hybrid of immediate and deferred revenue recognition.
The iPod touch was sold flat-out with immediate recognition before the new rules took effect, because there are significant downsides to deferred recognition. However, the iPad can take advantage of the new hybrid rules that Apple pushed through FASB, so it need not charge for major updates. OS 4.0 will be free. OS 5.0 might be free; it might not.
At some point, they have to bring in additional money to fund the software development, and that's where any charges above the first dollar or two go. 99 cents is a token charge for the rules. The $9 after that is to pay for the work.
EDIT: Incidentally, first generation iPhones are now fully accounted and were all sold before the new accounting rules took effect; this means that OS 4.0 will probably not be free for 2G owners (if it runs at all).