Absolutely. That's the way the system works. The users of the system pay the cost. For a number of years, it's worked very successfully.
The railways are not immune to drainage issues. Even though they might be up on a raised platform, there still needs to be drainage around them. The water still needs to get away. The water still needs to flow underneath railways so that they don't erode and cause issues with the infrastructure underneath them.
Railways are as big a user of the drainage system as any of us farmers or municipalities across Ontario.