I'm not sure where you're getting that number from. Here's a federal budget breakdown for FY2016 [1]:
Non-discretionary spending:
Social Security: $910 billion
Medicare: $588 billion
Medicaid: $368 billion
Other: $563 billion
Interest payments: $241 billion
Discretionary spending:
Defense: $584 billion
Non-defense: $600 billion
Spending on Medicare, Medicaid, Social Security, interest payments, and defense would not decrease if rural citizens moved to the city. Thus those subsidies aren't solely for rural America, so I won't include them in your "trillions of dollars" claim unless you want to make the claim that the government is subsidizing both rural and non-rural citizens to the tune of trillions of dollars, which nobody would doubt.The rest of the budget adds up to $1,163 billion dollars. Even if you made the wild assumption that all that money went straight into the pockets of rural Americans, it's hardly trillions of dollars.
(Note that I'm ignoring state budgets. But I think the trillions of dollars assertion is so absurd that I'm not going to waste the time to look up those stats as well.)
[1] https://www.cbo.gov/sites/default/files/cbofiles/images/pubs....