Fluttershy is just very quiet and delicate, there's nothing "sinister" about her. She's generally very patient, but she has her limits. She's also a doormat, so it's safe to assume that she has a lot of pent up resentment that eventually boils to a head.
There's an episode in Season 2 that covers this, but I won't spoil it for you.
There's also a lot of fan speculation that she's secretly a huge slut, but that's a different conversation entirely.
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