As president, there really isn't much he can do about them except tweet complaints and browbeat Congress.
Subsidies go to large agricultural corporations, they cost the taxpayers billions of dollars, and they distort the market. If they actually do provide some sort of safety net to the family farmer then that's a minor side effect of this government largess.
Fortunately, others see the problem. See The Insane World of Agriculture Subsidies and To Drain the Swamp, Trump Must Reform Agricultural Policy, for example.
Unfortunately, a lot of those subsidies went to companies in states Donald Trump carried. Conservatives, libertarians and independents would like to see a reduction in government expenditures. And a cut to the farm subsidies would certainly seem appropriate. But in his view, the farm industry may be one of those he thinks deserves a handout.
There are many in Congress who think farm subsidies are just fine. So it may be unrealistic to hope to see some reform. But we'll see.