Trivia: The two 'disc jockeys' in the soundbooth of the 'End of Line' club are actually Daft Punk, the French group that created the movie's soundtrack.
Trivia: In the first film, the street sign outside Flynn's Arcade indicates it's on Watseka St. In the second film, the street sign in front indicates the arcade is on Mead St. Also, the surrounding neighborhood seems to have undergone some redevelopment. This isn't really a mistake since a lot can happen in 28 years.
Trivia: After Sam hacks into the back door of ENCOM he comments: "Now that's a big door." Kevin made the same comment when he hacked into ENCOM's back door in the first movie.
Trivia: Two references to "The Black Hole", another Disney movie, can be seen in the film. There is a poster for "The Black Hole" in the bedroom of Sam Flynn in 1989 and an action figure of the Old B.O.B. robot is on his shelf next to the Tron action figures.
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.