I don't believe this is the result of an ideological belief. This is standard Apple app store policy that if you allow any sort of in-app purchases, they have to go through Apple.
So it's pretty clear that Apple does allow financial transactions to happen in apps, without taking a cut or anything. What's unclear is why they would allow this for Citibank, LevelUp, etc., but not for bitcoin.
Which is nonsense, of course. Things are legal unless explicitly made illegal.
My local bus service sells bus tickets through an iOS app and they have to give up 30% of the sale to Apple. Even major retailers like Amazon and B&N ended up removing in app purchases back in 2011 [1] to avoid Apple taking 30% of their business. They are not even allowed to link to their own web stores from their apps.
Frankly I'm just amazed Gliph ever got that functionality in there in the first place.
[1] http://news.cnet.com/8301-1023_3-20082925-93/apple-forces-am...
The in-app purchase rule only applies to virtual goods. A bus ticket, much like a plane ticket, should not fall under this rule. And, in fact, you are prohibited from selling real-world items via in-app purchase.
What you're buying isn't the virtual ticket. It's the bus ride.
My feeling has been that the major companies don't want to acknowledge Bitcoin yet and are waiting a bit to see how things play out. Not supporting it for a while won't hurt them too much financially. They lose some transaction fees but don't have to support a new payment type.