The law that created Amtrak provided for it to operate on tracks owned by freight companies, with usage fees, under the condition that passenger trains get higher priority than freight trains. Part of that condition is fines, payable from the freight company to Amtrak, for Amtrak train delays caused by the freight company.

Unfortunately, for various political reasons that part of the law has almost no teeth so freight companies openly flout it or treat the meager fines as the cost of doing business. It's a big part of the reason that passenger rail sucks in the US.

Amtrak doesn't even license it - Amtrak is actually owned mostly by the freight railroads.

The National Passenger Rail Corporation is a federally chartered corporation whose controlling interest is owned by the US federal government.

Yup. It's the rails underneath it that are mostly owned by freight or other rail companies.