I would have thought that the हूँ is still representative of "am" and therefore मैं खाता हूँ is "I am eating." Looks like I'm wrong.
हूँ(Hoon) is not representative of "am". It can't be directly said to be the counterpart of any english word. It is a verb form and can mean different things in different sentences.
Here the word "khaata" in conjugation with "hoon" makes the sentence "I eat." If you want to strictly assign a word to "hoon" here, you can consider the english version to be "I do eat" and say that "hoon" represents "do".
If it was "main kha raha hoon", the sentence would become "I am eating."
khaata hoon -> (do) eat
kha raha hoon -> am eating
thank you. It helps my memory if I can come up with english substitutions, even if they're not appropriate.
The habitual (I do) and progressive (I am doing) do not always map onto English in the same way. The default "textbook" translation is "I eat." But in some contexts you might use that tense in a way that sounds better in English as -ing. For example, you tell someone you're waiting for to hurry up and they reply "I'm coming!" But instead of saying "main aa raha hoon" they may actually say, "main aata hoon!"