That's just a difference in how it is though about. Many plates, especially older style plates, have a concave part where you put the food and a rim around the edge. We still say on a plate, because it is mostly flat, but I don't know if you would find it inconsistent if you had always been taught to say in.
Unfortunately, that's not how language works. TopClampet is correct. In Italian, it is the thing LIKED that is actually the subject of the sentence, not the liker as in English. So you will always see some form of a before what we think of as the subject of the sentence.
Since we haven't learned about pronunciation, and I doubt both the audio and my own ears: would there be a difference in pronunciation between 'nelle' and 'mele'? (Apart from the n/m, obviously). In Dutch for example the vowel sounds different when followed by two consonants rather than one, is it like that in Italian as well?