Ask yourself, in what part of the constitution does the "power" to regulate the railroad, or for that matter, any other business, emanate from?
Most would say Art I, Sec 8, Cl 3, the "commerce clause."
Even accepting that "conventional wisdom" that this clause does grant the power to Congress to "regulate" a private business (how did a "foreign nation", on of the "several states" or an "Indian tribe" become a private business?, the power still cannot be used to violate the Bill of Rights.
For example, by the "conventional wisdom" interpretation of the commerce clause, Congress can regulate the business of printing a newspaper.
But the Bill of Rights, Amendment I, specifically prohibits the regulation of the content of the newspaper.
The same constitutional principle applies to use of Congressional power when the taking of private property for public use comes into play.
If any notion is "specious" (having the ring of truth or plausibility but actually fallacious) it is the "private railroad crosses a public roadway" contention.
Free people adhere to the convenants of the constitution because if we do not then we have nothing more the a tyrannical democracy.
Let the railroad industry compensate the Federal government for the services rendered by the U.S. Army in the latter half of the 19th century (i.e., chasing the Indians all over the Great Plains). Then we'll sit around and pontificate about the virtues of private enterprise and the limits of Federal power under the U.S. Constitution.