It was pulled because the GPL license made Apple sad. Now it's MPL (Mozilla Public License) which Apple doesn't have a problem with.
http://thenextweb.com/apps/2013/07/18/vlc-for-ios-will-retur...
http://thenextweb.com/apps/2013/07/18/vlc-for-ios-will-retur...
The GPL itself is not a problem for them in general and they don't just go around removing apps that are licensed under it.
That's not true.
The problem was with the TOS that a user must agree to in order to be allowed to use the store. The TOS places limits on the user that are incompatible with GPL.