I think the theoretical idea is that we want to ensure that there is always a very large domestic corn supply, in the event of war or something. Corn is a crop that has a lot of uses; it can be refined into sugar, it can be used as flour, it's relatively energy dense food-wise, and it can be fairly easily converted into fuel if necessary.

I'm not saying I fully agree with the reasoning but I at least kind of get it.

right. view it instead as "we need to keep domestic corn production above a certain threshold." the result is that we have a lot of extra corn. now the question becomes: what do we do with this extra corn? we can either throw it away, or turn it into fuel.

it's not an efficient course if the target is fuel, but that's not the target. it is a decent use if we have lots of corn that nobody wants, which we do.