I would argue that there are a number of reasons why corn is highest on the list of subsidies.
First, there is the fact that corn is simply grown more than any other crop in the United States. As can be seen in this link, the value of the corn grown in the US is greater than the value of the next three largest crops combined. There is also much more acreage in corn than in any other crop. For this reason, if for no other, corn would logically be subsidized more than any other.
Second, corn is very important to the economies of a number of states. These are states in the farm belt and they have a great deal of clout in Congress. This helps to increase the likelihood that corn subsidies will continue to be high.
Finally, corn is not only used as a food crop these days. It is also being used for ethanol. This makes it more likely to be cultivated and more likely to be subsidized because we are trying to come up with ways to make fuels with less of a “carbon footprint.”
These are some of the most important reasons why corn subsidies are higher than any others.