Generally, no, railroad employees can't carry on the job. All the class-ones have a blanket prohibition on the posession of weapons by employees while on company property. Federal law (and that of most states, even ones with concealed carry laws) also allows companies to set their own rules regarding concealed carry by employees while on the job. In short, company property = private property as far as the employee is concerned. The law allows private property owners a lot of latitude in deciding what is allowable on their property. This can and does supercede any conealed-carry rights/priveledges the employee might have.
Just speaking for myself, there are two sides to every coin. I'm firmly in favor of concealed-carry, but I'm also in favor of the rights of property owners. So if my employer says no, then no it is. Also, railroads generally have an obligation to maintain a "safe" working environment for their employees, and I would think that would include some consideration to operation in bad areas. But then again, go ask most railroaders what they think of their company's dedication to that obligation to a safe working environment, you'll get an earful.