How do Holling's feelings about Mrs. Baker change from the beginning of the book to the end?

Initially, Holling thinks that Mrs. Baker hates his guts. The feeling appears to be mutual. The special one-to-one sessions he is forced to have with her are no such thing. To Holling, they're a punishment and a form of exquisite torture inflicted on him by a mean, sadistic teacher. Holling greatly exaggerates, of course, but there's no doubting his genuine loathing of Mrs. Baker.
In due course, however, Holling comes to realize that he had gotten Mrs. Baker all wrong. She never really hated him at all; she just wanted to instill some discipline into him. She also wanted to broaden his horizons by teaching him Shakespeare, which to Holling was even worse than doing menial chores. But thanks to Mrs. Baker's patience and persistence, Holling comes to develop a great love and appreciation for The Bard, which makes him look forward to his Wednesday lessons in a way he never thought possible.
On a personal level, Holling also sees a different side to Mrs. Baker. He sees the real person beneath the rather forbidding exterior. Holling eventually sees that Mrs. Baker is a good person and someone to be trusted and respected. Holling even goes so far as to pray for the safe return of Mrs. Baker's husband, who is missing in action in Vietnam.

Holling's feelings change from not liking Mrs. Baker at all to Mrs. Baker being his favorite teacher.  
In the beginning of the book, Holling has to stay in Mrs. Baker's classroom on Wednesday afternoons.  He has to do this because he is the only Protestant in a school full of Catholic students and Jewish students.  On Wednesday afternoons, both of those groups go to their respective religious studies classes.  
Neither Mrs. Baker nor Holling is pleased about the Wednesday afternoon arrangement.  Mrs. Baker starts off the first month by requiring Holling to do menial tasks like clean desks and chalkboard erasers.  Holling actually thinks that Mrs. Baker hates him.  In October, Mrs. Baker decides that the two of them will study Shakespeare together.  That's when Holling really believes that she hates him; however, over the course of the school year, Holling realizes that he likes both Shakespeare and Mrs. Baker.  He comes to see her as a person that wants the best for him.  This is evidenced from things she does for Holling like drive him to the professional baseball game when his dad forgets to pick him up.  She also arranges for Holling and a friend to play baseball with a couple of the Yankees baseball players.  By the end of the novel, Holling's feelings about Mrs. Baker have completely turned around.  He no longer sees her as an enemy.  He sees her as a friend, confidant, counselor, and wonderful teacher.