Flynn, as Yuri's friend and something of a rival, joined the Imperial Knights with Yuri. Yuri, who grew tired of the rules and regulations of the politically-minded knights, quit early. Flynn, however, stayed on board with the knights so as to try and change the broken system from within.
Flynn's past plays a role with his staying in the Knights even after his friend Yuri left. Flynn's father, Finath Scifo, was also a knight, but had died when he disobeyed direct orders given by his superior. His father's disobedience affected Flynn's mentality with receiving orders when he had first joined the knights with Yuri and had caused conflict between the two. Flynn, however, realizes that his father's disobedience did not lead to his death in vain when Yuri tells him he did leave something behind that he wanted to protect. Trying to live up to his father's legacy (that he is now proud of), Flynn has a very strong sense of duty and following what he believes is right without question.
While their goals may be the same, Flynn and Yuri have very distinct ways to achieve those goals. Flynn is very much a play-by-the-rules and using-the-system correctly kind of person while Yuri will achieve his goals through any means necessary. As a result, Flynn is conflicted as to whether aid Yuri in his journey or arrest him for his crimes.
Visually, Flynn was designed to resemble previous Tales protagonists. In addition to this, he is able to use the "Demon" line of artes skills, which are usually reserved for those characters. Ironically, the game's actual protagonist, Yuri, is not able to use those skills.