"You agree that the terms of the Licensed Application End User License Agreement will apply to each Apple Product and to each Third-Party Product that you license through the App Store Service, unless the App Store Product is covered by a valid end user license agreement entered into between you and the licensor of the App Store Product (the “Licensor”), in which case the Licensor’s end user license agreement will apply to that App Store Product."
Read the unless part...
Oh, of course, it is better to make a political statement that doesn't even read the AppStore terms... Not to mention that VLC is GPLv2 not GPLv3...
The FSF addressed that back when GNU Go was the program getting pulled. They pointed to the section in the terms that said this:
The Usage Rules shall govern your rights with respect
to the Products, in addition to any other terms or
rules that may have been established between you
and another party.
They noted that it said it was in addition to any other terms between you and another party, and so the Usage Rules still applied EVEN IF the license of a particular program said otherwise.
However, looking at the latest version of the rules you cited (which is the same link the FSF cited), I don't see that language. The FSF published their more detailed explanation of the GNU Go problem, including the above explanation of why the Usage Rules still apply, on May 26th, and Apple updated the terms on June 21st.
On first glance, it appears that Apple may have in fact addressed the problem and GPL software is OK on the store after all.
The real question is how did Apple's QA that checks apps for the store not catch the problem beforehand? VLC is easy to Google, and GPL 2 license isn't tricky to find. I'm sure Apple has plenty of lawyers and computer people that are involved in checking licenses, so they should have either an argument stating why they believe they are in compliance, or they shouldn't have let the app in.
If there's a problem, why was the app submitted? Did the problem appear after the app was submitted? If not, if the problem existed at the time the app was submitted, then the app ought not to have been submitted.