I'd say the best way to think about this question is scale. Quarks are part neutrons and protons. Those are parts of atoms. Atoms are parts of molecules. Which are in everything you see.

So if some one asked you to make cookies you'd think "oh, I need sugar, butter, chocolate chips, flour but you might not think "I need atoms, protons, quarks, and molecules which combine in the way to make the ingredients I need"

So when atoms are referred to as "the building blocks of matter" it's not incorrect, it's just that they have building blocks of their own!