Pretty sure you can't charge a railroad a toll for passing through their jurisdiction - but I don't have a citation.
Fines for blocking crossings are common, on the law books. However, I think that assessing those fines is spotty. And, even if tickets are issued, the fine levels are too low to encourage the RR to change their practices - it is cheaper to pay the fine than to change the way they operate. Given that RR companies have paid lobbyists, and contribute to local and state campaigns, and that Joe and Jane Motorist do not, this is highly unlikely to change.