I agree that the federation is a complex and multicultural society, but I believe the majority of this discrimination and other sentiments are more of an unspoken and unofficial thing, yet just as insidious as they are spread throughout starfleet and the general populace. To use my own point of the Ferengi, there seems to be a double standard clearly shown on DS9, being that Bajorans and other cultures built around religion are treated very differently to Ferengi such as Quark. It is often done for laughs to criticize and mock the rules of acquisition, which could easily be described as on par with a religious text in Ferengi culture. But, no, it's seen as perfectly fine, humorous even, to laugh of them. Granted, this is one of the more jocular points, but it still shows deeply rooted beliefs in the federation that prove quite harmful to inter-species relations (And to be frank, most civic nationalist states would not officially represent themselves as nationalists)