So I just beat the game tonight. Since Booker is Comstock, why does he turn into such a racist asshole? I think early in the game it's alluded to that he (Booker) is not racist. I guess the easy way to explain it is that was the best way to form a cult at the time?
Booker's racism comes from the earlier Indian War, and the allegations made to Comstock/Booker in one Comstock's voxophones indicate that he was accused of being part Indian. To prove himself, he butchered, scalped, and burned teepees with people inside them.
The guilt which he felt afterwards led him to the baptism event, but with it, Comstock, feeling that he is given free forgiveness by a greater power than himself, without putting any real effort into being a better person, continues his racist progression because he justifies his work as being led by divine purpose.
Meanwhile Booker, feeling regret but unable to go through with the baptism due to not believing in such forgiveness for his heinous actions, slowly comes to terms with what he did, or at least tries to via marrying his wife and having Anna, but after losing his wife, his despair builds up into large debts due to alcohol and gambling.