I think it is important to remember that the ideas of Booker T. Washington is not the only ideology or philosophy that is disparaged. In fact, the novel as a whole lampoons the various general ideologies of people, showing how they limit the identity of the protagonist. Again and again, the anonymous protagonist of this story discovers that the ideologies adopted by groups and institutions, when compared to the reality of the racial situation in America at his time, are too basic and simple in order to support him in his quest of establishing his own identity. This fact is as true for the ideas of Booker T. Washington as it for more separatist and violent ideas, such as those espoused by Ras the Exhorter.
However, perhaps the novel is most clear on this point when it introduces the Brotherhood, which promises to liberate "the people," though, as subsequent events clearly demonstrate, all it actually does is to restrict and betray the freedoms of the same "people" it professes to save. The lesson of this novel therefore is that human identity and life is so complex that there will never be one overarching ideology that is capable of encompassing the massive diversity and richness of what makes us human.
Therefore, just as the narrator's college experience points out the glaring limitations of the ideas of Booker T. Washington, we need to be aware of how the novel challenges and disparages all such ideologies that claim to provide an all-encompassing framework for human experience.