Several apps use other forms of payment: Groupon, eBay, Gyft, etc all take alternate forms of payment. The limitation Apple places is that 1) If the origin of the payment or subscription is from the app, the app must use iTunes (and Apple's 30%). 2) Alternate forms of payment (such as Amazon and PayPal) are allowed, but sign up and referrals cannot be redirected by the app.
Summed up: If the app is where the payment's source occurs, it must use iTunes. If there is another form of payment, the other form must be registered externally PRIOR to the app purchase.
It's confusing as heck, but Apple hopes that the users and developers will mak things simpler by just using iTunes payment in their apps.