Is Emily's father protecting her and if so how?
This is a great question and while there is no right or wrong answer, as I read carefully, I have a sneaking suspicion that Emily's father was not so much protecting Emily as much as he was trying to keep her around to take care of him.
According to the story, Miss Emily's family had been part of the aristocracy of the town, and no suitor "was quite good enough for Miss Emily...". But later on, the narrator says that they "remembered all the young men her father had driven away..." and still later refers to "that quality that had thwarted her woman's life so many times...".
In those times, and sometimes even today, families had an expectation that one child will remain at home to take care of an aging parent or parents, and this was inevitably a female. It appears that Miss Emily was an only child and that her mother was long gone, so her father is likely to have manipulated to make sure that she was not "taken" by a suitor and could remain to take care of him.
Additionally, there are several references in the story to insanity in Miss Emily's family. Her father might have used this history to scare of suitors or might have been insane himself in some way that caused him to keep Emily at home or that required Emily to stay at home.