From an out of universe perspective it was because she was an audience surrogate.
To a child the world can see harsh and arbitrary. Adults can seem overly prescriptive, and criticism can seemingly come out of nowhere for reasons that they don't understand.
Having authority figures who are inherently - and obviously - unreasonable invokes a sensation of kinship and an emotional attachment to the lead character in children who feel that they are punished simply for being children or for doing things that children do.
From an in universe perspective, it's because she is essentially honest and innocent. While her family are greedy and see honesty as a sign of weakness. Her father in particular spends his days scamming people (for example, filling car gearboxes with oil and sawdust to stop them from making a noise, or winding back a vehicle's mileage to make it seem newer).
He sees her book smarts as being a waste of time because they won't enable her to do what he does, but he also feels threatened by them, because he spends most of his time dealing with directing people away from problems (misdirection to conceal them) while she is both capable of seeing through his misdirection and putting forth actual solutions to the problems that he is seeking to hide.
He also begrudges the fact that she doesn't contribute to the household, she takes but never gives. At least not things that he sees as being useful.
More so, when she takes he is obliged to give because she is his daughter. He is perfectly OK taking from other people because he sees himself as smarter than they are and more deserving than they are. He tricks people into buying poor quality vehicles so he believes that he is owed what he gets from them, whereas he has to provide for Matilda because she's small and can't provide for herself. He sees this as being the equivalent of stealing from him.