The Trunchbull holds everyone at school captive just by her threatening presence. She can also literally confine people in torture apparatuses like The Chokey, or force them into signing legal papers against their wills. Characters like Miss Honey and Matilda are imprisoned by their family situations, but Matilda ultimately uses her mental powers to free them both. What's more, as soon as she's able to read on her own, Matilda develops the ability to escape from her surroundings whenever she wants. All she has to do is open a book. And that's the beauty of Matilda. Sure, these characters might be trapped by their unfortunate situations, but the key to freedom lies within themselves.
Miss Honey doesn't have what it takes to free herself because she's too old. She has to rely on Matilda's youthful imagination to help her escape the Trunchbull.
Miss Honey should have stood up to the Trunchbull ages ago, because by not doing so, she is allowing the evil headmistress to literally imprison kids. Not cool.