"Maybe we could have continued to be friends. But not in this story. I've decided to make a brave decision like you taught me to, and say goodbye.

— Fluttershy"

Fluttershy wrote letters that formed a journal to give one day to Rainbow Dash. She has written it throughout the majority of their friendship, relationship and heart break. Now was the time she was going to give it to her. Not because she wants Rainbow to know she still loves her, but because she wants Rainbow to know how much she has hurt her. Besides, she doesn't have to stick around much longer anyways as she's planning to move away.