Let's run down the kid's lit checklist: we've got a youthful protagonist, a school-related plot, some adult antagonists, and pranks (involving newts and itching powder and hair dye). And even though she's five, Matilda's worried about things that many other kids' lit protagonists are worried about:
Of course, as soon as you're done reading Matilda, you know the answer to all those questions is "yes."
This whole telekinesis deal shoves this book over into the fantasy category, too. Things happen in Matilda that don't have scientific explanations or can't be easily explained:
Maybe the most fantastic of all is the idea that an administrator as outrageously terrible and abusive as the Trunchbull would be able to hold on to her job without any problems. That's definitely the stuff of fantasy.
Okay okay, so the heroine does stay five years old for the entire story. So why are we calling this one a coming-of-age story?
Because Matilda's mind matures at a ridiculous rate. Her brain grows up really fast. Miss Honey says she's "'not really a child at all because [her] mind and [her] powers of reasoning seem to be fully grown-up […] we might call [her] a grown-up child'" (17.12). From her beginning as a timid young girl, we see Matilda learn to read, develop psychic powers, and help rescue an innocent person from a tyrant, all of which she accomplishes by the end of the book. So even though she hasn't quite gotten there physically, on the inside, she's definitely all grown up.