There is some incorrect reporting on this from a few different sources.
Check the Videolan blog for what's really going on.
The problem is that Apple's psychotically restrictive EULA for their app store puts too many restrictions on software downloaded there. It's not GPL compatible, and Apple is not willing to make it compatible for different licensing models. (Go figure.)
It would be simple for Apple to allow GPL software without compromising anything of their own. They simple have not done so, which, to me, indicates that they simply do not care about their users or developers in the least.
VLC is the first fallout.
Java is different as Oracle owns the copyright and can do anything they want, GPL or no GPL.