We've got the entire written word of the creator of the universe in our hands to learn from. So why do churches think they need to play movie clips to make a point? There is no logical reason except that they are pointing their services toward the secular lost. Yet if you read the new testament, the purpose of the gathering of the believers was to edify the believers.
Yes, and this believer is not edified by seeing movies in church. Not at all. Nor do I think it is an effective way to reach the lost. The movies were made to mean what the producers, directors, and screen writers intended them to mean. Twisting them into some sort of spiritual context is just ridiculous and offensive.
Actually, using movie clips (like what I saw of the use of the scene from The Matrix) is kind of a modern equivalent of using analogies or parables. It is a way of explaining a thing people don't understand too well through something they do.
At the time the Matrix analogy was being used, the movie was extremely popular. The whole audience had seen and liked the movie. The scene had an obvious context and the youth pastor exploited it to help young people understand that the Christian life is more "real" than the so-called "real world." On a side note, it completely changed the message of the movie (which they had already seen) as well.