Mi estas komencanto, but I will try to explain it how I understand it.
"Kion" is used in the accusative case.
So... "kio" is used for a questions such as.. "what is it?" where the answer is a straight forward "it is a..." (the answer has a subject but no object).
However, "kion" is for questions where the answer will include an object(s). For example, in this case, "Kion vi manĝas por matenmanĝo?" will require an answer such as "Mi manĝas ovojn por matenmanĝo."
You can see we use -n in "ovojn" because it is the object in the sentence, while "Mi" is the subject. For the same reason, the "what" in this sentence requires the "n" as well.