When she was a Wonderbolt trainee, she may be considered a neutral character (despite being reckless and disregard for the safety of others), but the dilemma begins with Siege of the Chrystal Empire comic and Fluttershy and the fine furry friends fair book.
In the comic, she works alongside two of the most tyrannical villains (King Sombra and Queen Chrysalis) to attack the Crystal Empire and fight against the Mane six and the princesses.
In the book, it's mentioned that she is hanging out with Rainbow Dash, and looks like they are still friends.
At the end, it's difficult to know her position about being good or evil.
What all do you think?