The conflict that develops between the narrator and the Brotherhood is part of a much bigger theme in the novel that we can see elsewhere in his life. This theme points towards the limitations of any one ideology in trying to capture or provide a framework for the rich diversity of human experience. Again and again, the narrator, as he ventures through life, discovers that the various ideologies adopted by institutions and groups possess massive gaps or are too simplistic when trying to capture or serve the richness of human identity.
This is as true for the ideas of Booker T. Washington as it is for the separatist ideology expressed by Ras the Exhorter. However, particular focus is given to the conflict that the narrator experiences with the Brotherhood. Although the beliefs of this group seem to promise so much, and initially the narrator is taken in by their claims that their beliefs will save "the people," gradually, both we and the narrator see that something very different is occurring. In fact, the Brotherhood is shown to systematically betray and restrict the freedom of its members.
The crux of this theme is expressed by the narrator in the Epilogue when he reflects on his life and how he has lived it:
And my problem was that I always tried to go in everyone’s way but my own. I have also been called one thing and then another while no one really wished to hear what I called myself. So after years of trying to adopt the opinions of others I finally rebelled. I am an invisible man.
The narrator explicitly draws attention to the problematic nature of believing the ideas and signing up to the ideologies of others without specifically working on your own identity and beliefs. The conflict that he experiences with the Brotherhood is a major example of how we cannot trust one group or ideology to give us our identity.