"My favorite fruit is THE apple." or "My favorite food is simply AN apple."
Apple alone - without "the" sounds like a type of taste (a descriptive word rather than a proper noun.) "Apple is my favorite kind of pie' or 'when it comes to candy, my favorite is apple."
Finally, "are apples" could be made correct in this way:
"My favorite things to eat are apples." In this sentence, we have a plural object (pronoun things) and a plural auxiliary verb (are). Notice in your sentence, you have food (singular) and are (plural)... and yes apples (plural). Try to keep it consistent with the subject rather than the object. With a little study, you will quickly lean to see the difference.
Food - is - apples - OK
Food - is - an apple - OK
Food - are - apples - not so ok