The nature of the question is a little too broad to answer. "Intermodal Transportation" refers to pretty much everything, so your question is really "what kind of taxes do truck, rail, ocean and airplane transport companies pay?" The answer is a lot of them and they vary by where the company operates, sometimes down to regions, individual states or facilities. For example, there is (was?) anti-mafia legislation that levies an additional tax on trucking which is initiated within a 50 mile radius of New York City in response to mafia control of the trucking industry in that area.
Is there a specific sector that you're interested in? I doubt anyone here can answer the question comprehensively, if you really need the information you'll need to pay someone - lawyer or CPA probably. Maybe both.