Among other things, the purchase of service agreements currently in effect on Metra's UP and BNSF lines requires the host railroad to submit an annual operatiing budget covering the cost of providing commuter service at the same level as the previous year. Metra will usually approve the budget, as long as they keep getting at least the same annual share of state and federal monies. If there is a decrease from these funding sources for any reason, Metra will then ask for a reduced budget from the host railroads. At the end of the year, Metra pays the host railroad the difference between the approved budget and the passenger revenue. Metra also compensates the railroad for allowing Metra traffic to operate over their lines.
Within the contract, the purchase of service agreement also stipulates that Metra is responsible for the funding of commuter-related capital improvements, which include the procurement of new rolling stock, physical plant upgrades (track, switches, signals, etc.) and station projects. In return, the host railroad shares the cost of the capital projects that benefit freight operations, which are normally those associated with the physical plant.
For addtional clarity, the following link describes Metra's ownership and/or contract relationship on each of its routes. Note that for the NCS and HC lines, the trackage is now operated by Canadian National...
http://hometown.aol.com/metrafan/rrmetra.html