system
Given the following post, respond as if you're commenting on Reddit:
human
[Star Trek] What's the level of xenophobia in the Federation and Starfleet?

Is it mostly directed toward enemy species like Klingons and Cardassians and Romulans or is there a consider fear or hatred of non-threats like say the Ferengi or even members of the Federation?
gpt
Overall, it's extremely low, but not nonexistent. The Federation was literally founded on a basis of rejecting xenophobia and embracing the differences between individuals in order to make a stronger whole. In its early days, there were certainly problems as the various species worked with each other in ways they never had before. Part of the reason Earth was chosen as the capitol world was because it was neutral ground, and would solve many of the old animosities and xenophobic issues of some other founding members. For instance, the Andorians would have never joined the Federation if the Vulcans hosted the seat of power. But the longer it existed as a single entity, the less those issues mattered until they mostly disappeared.

Starfleet is slightly different. A lot of ships are crewed largely by a single species, probably for ease of environmental control and communications in light of a catastrophic technological failure. (if the universal translator fails, everyone can speak the same language and understand each other's social cues in order to solve the problem without incident) So a lot of cultural prejudices can spread through a ship through a handful of individuals. Consider Captain Solok's all-Vulcan crew supporting his odd racist vendetta against humans. 

On the other hand, most everyone in Starfleet has been raised in the Federation's overall culture of open acceptance. So it's still overall quite low, and is mostly down to an individual level. Miles O'brien had problems with Cardassians, but it was because of his trauma surrounding a recent war, not an ingrained xenophobia against individual Cardassians. 

On the other hand, there are a few notable examples of larger animosity. Humans still hold the Romulans in low regard centuries after the Earth/Romulan war. (and the later centuries of backstabbing/treaty dodging) And said tension was one of the reasons the Federation was so lax in its response to the supernova that destroyed Romulus and crippled the Empire.