If all the railroads have to abide by Amtrak's rules then it's a level playing field and they can raise freight rates as needed to maintain return to investors. The notion of "theft" is not so clear when we're talking about infrastructure that lays all over and along the the land we all live in, not to mention the history of how that right-of-way was acquired. As long as there is bright line law and it's fairly administered, the railroads should not have a veto on reasonable passenger service. Now that's a big "if," that it's fairly administered, and that it does not advantage other forms of transportation and their deals with the government, etc. (All transport has deals with the government, perhaps railroads the least.) Ironically since there are so few major rail companies, it would be somewhat easier to monitor such bright line rules, than it is, say, seaport public-private authorities, or airport ticket tax allocation, or varying trucker diesel taxes and tolls.
The middle ground between stifling government intrusion and your concept that they own it, and we pay what they ask or it's theft, would be how the states negotiate with the railroads to get increased passenger service. In other words, paying for upgrading the Acca freight yard to get more passengers on CSX in Virginia, and another infrastructure layout for NS to extend to Roanoke. The dollar amounts of those deals are a lot less clear in their fairness than just requiring the freights to prioritize Amtrak as rule, the same for all companies, with a rate that can litigated if necessary.