For infrastructure improvements. Here’s one article:
The Shellpot Bridge Replacement isn’t the Feds but rather a State DOT project:
http://ops.fhwa.dot.gov/freight/publications/freightfinancing/sect3.htm
I would agree that any payments by a government entity for railroad infrastructure inprovements which are intended for the commercial benefit of the railroad (as opposed, say, to safty of the public at intersections) are subsidies and should be prohibited.