Kevin Flynn: It's amazing how productive doing nothing can be.
Kevin Flynn: The only way to win the game is not to play.
Kevin Flynn: Your old man's about to knock on the sky and listen to the sound.
Kevin Flynn: The Grid. A digital frontier. I tried to picture clusters of information as they moved through the computer. What did they look like? Ships, motorcycles? Were the circuits like freeways? I kept dreaming of a world I thought I'd never see. And then, one day...
7 Year Old Sam Flynn: You went in?
Kevin Flynn: That's right. I got in.
Kevin Flynn: Life has a way of moving you past wants and hopes.
Clu: I'm not your father, Sam. But, I'm very very happy to see you.
Sam Flynn: Dad?
Kevin Flynn: Sam.
Sam Flynn: Long time.
Kevin Flynn: You have no idea.
Answer: Because Clu was given all the authority of the most important user, the creator, Flynn.
Phixius ★
But what did Clu do to Tron to make him serve him? Tron fought for the Users so it would make no sense for him to suddenly side with Clu who wanted to create the perfect system and help him in annihilating the ISO's.
When Clu and co. attacked Tron and Flynn, Flynn's disc must have been damaged, removing his personality in a way similar to amnesia. This allowed Clu, now master of the system, to gain control of Tron's skills. Later, when Prinzler saw Flynn, he remembered him and what he did, and regained his original purpose.
The answer was in the movie itself. During a conversion between Sam and his father it is mentioned that Clu had the ability to repurpose programs. This is the action that allowed him to "build" the perfect system. The isos were manifested without creation from anything and had genuine freedom that Clu couldn't repurpose. This is why he destroyed them because it threatened his strategy to create perfection. Answer: Clu repurposed Tron to serve him and do his bidding. That simple.