Continuity mistake: Quorra's suit has a light stripe running down its right leg. When she's captured by Tron, the light stripe is now on the left leg. This is most likely a flipped shot as her fringe/bangs are also slanting the wrong way. (01:33:50)
Continuity mistake: Throughout the movie Quorra is seen wearing high heel wedge boots. During the fight scene at the club she is shown wearing a different flat soled boot. Immediately after the fight ends she is seen in the high heel wedge boots again. (01:17:20)
Answer: Because Clu was given all the authority of the most important user, the creator, Flynn.
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.