"The Knight's Tale" follows the story of two men who fall in love with the same woman, and how one of them eventually wins her. The story focuses equally on both men. When Theseus releases Arcite from prison, for example, the tale not only details Arcite's woe at losing sight of Emily, but also takes time to comment on Palamon's anguish at the thought that Arcite might get to her first. In their brief period of separation, which isn't long, the tale shuttles back and forth between the two pathetic lovesick knights. And before their joust, we get to hear the prayers of both Palamon and Arcite.
Basically, the tale is refusing to allow us to take sides. Part of its point is that both Palamon and Arcite are deserving, noble knights who, as Theseus says, are worthy to marry a woman like Emily. Accordingly, both of them serve as protagonists.