[tgsovlerkhgsel]

It's almost as purjolok said, but actually even simpler. You don't bother taxing the goods, and not even the train company!

The diesel fuel that the train company will buy has already been taxed at the refinery (if it's a diesel train). The gas that the power company will burn to generate power for an electric train has been taxed at import. The train company will simply pay the price of these goods, tax included, and pass this cost on to the owners of the goods being shipped. How is up to them.

Likewise, the "hidden" emissions from the production of the train are likewise "hidden" in its price: The steel that the train was made from was already taxed when it left the steel mill (not 100% familiar with steelmaking, but this may be one of the cases where it's insufficient to just tax the inputs since the steel mill might emit GHG that don't just come from fuel). The cost of the energy used in processing that steel already contained the cost of the emissions tax that was initially levied on the fuel. etc.