Well, keep in mind that it is Nailer himself who is the hero in this novel and it is Nailer's dad, Richard Lopez, who is the antihero. Richard Lopez has already lost his wife and began abusing drugs and alcohol (as a result?) in addition to his incredibly dangerous personality. Richard Lopez is also good with a knife and has many scars to represent knife fights. Nailer often escapes the beatings from his dad by cowering.
Getting back to your question, though, no, I don't think "Nailer's dad has anything against black people" due to Nailer's friend Pima. It's just that Nailer's dad had already gone wrong due to the effects of both alcohol abuse and drug abuse. (I suppose, in reality, there is no way to tell Richard Lopez's actual beliefs due to the effects of the drugs poisoning his body.) Nailer's compassion can be contrasted with his father's lack of compassion. Here is a good example:
Pleas spilled from [Nita's] lips, a desperate trickle. She was broken, soon to die, but still the words slipped out in a steady whisper. Tum Karuna ke saagar Tum palankarta hail Mary full of grace Ajahn Chan Bodhisattva, release me from suffering...He drew away. Her fingers slipped from his cheek like orchid petals falling.
Keeping this quotation in mind, there are also a few events in the novel that can help prove Nailer's dad doesn't hold a grudge against Pima either personally or because of Pima's race. First, Pima's mom did save Richard Lopez. This would lead to at least some positive feelings for Pima. Further, Richard Lopez (kind of) repays this debt when he, in turn, spares Pima's life during the fight for the rich girl, Nita. For Richard Lopez, survival is the key. For Nailer, he is willing to sacrifice that same survival in order to live with honor and without betrayal.
Well I highly doubt it! Nailer's dad is always under some type of influence so if he is aggressive towards Nailer it isn't because he hangs out with Pima; he's a drunk and a drug abuser. There is also the time Pima's mom saved Nailer's dad once and he spared Pima's life when they were fighting to keep the rich girl alive. The fact that Nailer hangs out with Pima or her being black has nothing to do with how his father reacts/treats Nailer but more about a support system in a world where survival is key.