Well, it is their platform and their store. If you think the rules are unfair then you can also develop for other platforms.
First, Apple had ZERO problems with approving VLC and getting it on the store. The app is gone now, but that is not because Apple changed their position, they simply responded to an alledged copyright/license issue reported by the original owner of the code.
The reason that the app has been removed is because the VLC developers, specifially Rémi Denis-Courmont, has requested Apple to remove the app from the store because of what license conflicts.
They would respond in exactly the same way if the GPL were not involved.
Seriously, Apple is currently working in the best interest of the claimed rights holder of VLC: it removed the app so that VLC and Applidium can figure this out.
This is not a case of Apple Against GPL: As soon as Applidium and VLC think they can actually work with the terms of the GPL and App Store then they can send that message to Apple and resubsmit the app.
I sure hope they do, but from what I've seen so far, the VLC folks seem to be extremely anti-Apple. We all lose. Thanks VLC.