What could she do ?
She was the most shy of the Shy family. She was more shy than her mother. She was also convinced to be the most shy pony in all Equestria. And she wasn't really wrong...
So, what could she do, exactly ? When she was in love with somepony ? Ask this pony to be her special somepony ? It was out of the question. No. She couldn't do that. Rainbow Dash would hate her.
Yes. Because the pony in question was the awesome, courageous, confident, perfect Rainbow Dash. Well, it's true that Fluttershy did get angry against her, but she couldn't love her less. Rainbow was her everything when she thought about it : she was her childhood friend, but also her savior. She gave her her cutie mark without even realizing it. She saved her so many times, she helped her with her brother, and to gain some confidence. She wasn't this close with anypony, not even Discord. Fluttershy couldn't explain why, but Rainbow made her fell complete when they were together. And when they weren't, she couldn't help but to think about her.
So she decided to just... Stay friend. For them. For herself.