I'm not sure Mattie dislikes all of John Milton, but she for sure doesn't like Milton's Paradise Lost. She doesn't like it for the same reason a lot of people don't like it. It's a bummer of a read. It's not about the fun, exciting parts of the Bible. It's about Adam and Eve's temptation, fall into sin, the fall of mankind, and the expulsion from the Garden of Eden. That's not exactly a high point for human history.
Mattie loves reading. She's a voracious consumer of literature and a girl that loves to learn. Her great loves are things by Dickens, Dickinson, and Jane Austin. One of her favorite books is Little Women. The common thread in the literature that Mattie loves is that it tends to portray women in a very positive light. It tends to emphasize female learning and empowerment. If the books are not female centered, then they at least focus on characters improving themselves through the advancement of their learning. There is positive growth in the characters.
That is not true of Paradise Lost. At its core, it is a story about two people who eat from the tree of knowledge of good and evil and are punished for their pursuit of knowledge.
Unfortunately though, I believe that Mattie's own experiences are closer to Milton's tale that the other stories. As Mattie grows up and comes of age, she learns more about the people and deceptions around her. She discovers men's affairs while being married. She discovers that people will kill for love. She discovers that defending right from wrong (racism) can have bitter consequences. In the same way that Adam and Eve lost their innocence through knowledge, so does Mattie.