Why are the witches or brujas usually women?
I can't remember a story involving witches that were not women, so one could say that is just the popular conception of what a witch is, both in Bless Me, Ultima as a novel, and in popular culture both nowadays and in the 1940s Latino Southwest. So one answer could simply be that it is traditional for witches to be women.
Tenorio's daughters, the brujas in the story, represent part of the evil that Ultima and Antonio's family must deal with, but Tenorio himself also represents evil. Nowhere in the novel does Anaya refer to Tenorio as a witch, though.
Some people think Ultima herself is a bruja, albeit a "good" one, while others recognize her as the curandera healer, a medicine woman. This role, the curandera, is a holdover from native culture that blended with Spanish Catholicism to survive to the modern day. There are students in my classes who have read the novel that say their mother took them or a family member to a curandera here in the Yakima Valley, while others who are more traditional Catholic still view them as brujas.