Because Iowa farmers get to vote on federal matters, but they don't get to vote in SF and NYC.

When I worked at Climate Corp, it was pretty interesting to hear the (nearly universally) Republican farmers argue for why there should be farm subsidies. About half wouldn't even try to justify it, and just said if the money's there I'll take it.

In this case, it's because Archer Daniels Midland can afford to buy enough federal representation to get the subsidies.

Sugar producers care more about the issue (because they get all the subsidies) than voters (for whom the subsidies are a small percentage of their tax bill). Plus, the subsidies represent a positive return on lobbying dollars, because there are a relatively small number of people to bribe. Sorry, I mean support.

This, however, was put on the ballot by local supervisors, and will be voted on by SF's population at large. That's a much harder dynamic to influence with money. Not that they aren't trying.

The government is not a single entity. There are various groups and conflicting interests, and it can be easier to do something that goes against a powerful lobby's interests on a local level. Corn subsidies are also meant to lead to stable food prices, which is something that benefits governing politicians. There are various conflicts of interest at work here.