To me, the song sounds more like it's about someone who's very manipulative. "Show me how to lie. You're getting better all the time". This guy is trying to gain power, and is taking down anyone in his way. Using lies and deceit, he turns everyone against those who are in his way, and no one knows that all along, it's really all just him. The one singing is as someone who can see what's going on. He says "There's something in your way" and then "If you can't get what you want, it's all because of me", implying he's finally going in to stop him, but even he falls prey to this guy's tactics with "Man I never had a chance".
And "lord of the flies" is a reference to Beelzebub, which is one of Satan's other names, and sounds like the one singing is likening this power-hungry, manipulative person as Lucifer, because he did the same thing when he got 1/3 of God's angels to turn against Him and follow the lord of flies instead.
And all the while, the singer is saying "Nice work you did. You're gonna go far, kid", meaning that with his tactics and his ability to utilize them, he will go far, because in this world, you get ahead by stomping others down.
The music video is not always indicative of the message. Many have absolutely nothing to do with it.
