Between Jem and Atticus, it is Atticus who carries more of the novel's action and stands more definitively as a representative of its themes. In a way, we can argue that Jem is a double of Atticus, but of a lesser stature. Jem learns the lessons that Atticus teaches, that is true. But Atticus teaches by example as much as a he does through words, so we can say that he articulates the novel's themes in multiple ways.
Certainly, Atticus Finch acts as the catalyst for several of the "epiphanies" that Scout has throughout her narrative. For, she has, indeed, learned to go inside another person's being/skin and see things from this person's perspective, and she has also learned to become more objective and cerebral, rather than giving in to her emotional reactions to circumstances.
I agree that Atticus has much more to offer to both the reader and his children than Jem. Readers and Atticus' children, alike, can learn from the lessons taught by Atticus. Therefore, he is by far the most important protagonist in the novel.
Atticus, due to his class, background, colour and profession has power and respect within society and among his peers and townspeople. He can get things done - people listen to him. Unfortunately, in those days this was a highly desirable position to be in and one which was nigh impossible for underprivileged groups to aspire to - we see this huge social divide and the ignorance it brings, in the novel.
Atticus functions as a protagonist in the sense that he is an active force in the novel in ways that Jem simply is not. The courtroom scenes are crucial to the book, and Atticus is at the center of them. Atticus, because of his age, talents, and status, as able to affect the action of the novel is ways that Jem is not.