To me, the subsidies that farmers receive is yet another example of how government taking taxpayer money and giving it to people/businesses can lead to outcomes which a majority of people don't approve of. I hope this example makes people more likely to entertain a deontological objection to any kind of government subsidy.
I deal with this problem by donating (almost) exclusively to animal welfare charities. Besides, I think that the suffering of animals reared for human consumption is much more intense than those of humans, in general.