Since Flynn went into hiding off Grid, there's a good chance that he is staying off the Grid (which is part of the reason why CLU hadn't found him and his disc for "over a thousand cycles"). Plus, it's suggested that not only vehicles malfunction when they go off-grid, but that programs and ISOs can cease to function properly by doing so (this comes from the closing scene of the video game, when after the Recognizer crash, Quorra's circuitry is seen flickering, almost as if it were on the verge of dying, but after Flynn takes a hold of her hand, it ceases to flicker and glows normal again). So, even if TRON wanted to look for Flynn, there'd be no way for him to do so because going off-grid in combination with the damage that TRON took, could possibly lead him to completely derez. Not to mention the fact that Flynn thought TRON was dead, as did everyone else apparently (as we get with the series) and since TRON was damaged, there is a tactical advantage: if everyone thinks you're dead, then there's no one looking for you. Plus, there's the possibility that if CLU knew that TRON was still alive, that CLU would hang back and keep an eye on him in hopes that he'd lead him right to Flynn. So, TRON probably wouldn't have looked for Flynn in order to protect him.
Plus, there's a good chance that Flynn did hear about Beck or probably heard about TRON but decided to stay off-grid for his own safety (and there's a chance that anything he's heard about TRON he would probably be hesitant to believe because there could be a chance that CLU may have purposefully spread false information to try to draw Flynn out of hiding). After all, Flynn did say to Sam in the film that there was a revolution forming on the Grid, and he did seem surprised when he discovered TRON being still alive. Not to mention, there's a good chance that Beck didn't tell anyone about TRON being alive in order to protect TRON, but when Beck eventually failed (which he obviously did, as we already know that his actions didn't do as much good on the Grid, as CLU was still large and in charge), TRON may have been with him, and instead of derezzing him, he reprogrammed him to be Rinzler and derezzed Beck, hoping that it would squash any further uprisings.