Apple can't stop you from using their products in a movie. Trademarks only protect brand confusion, nobody is going to watch Transformers 17: Age of Voltron and think that the whole movie is an apple product because a robot turns into a iPad.
It's just a case of "if you don't use our product this way, we won't do cross promotions or pay for product placement with you anymore"
* SPOILER AHEAD *
While Apple will let you use an iPhone on film, they won't approve it being used by a villain.