Okay, seriously, when was the last time you saw a train in the MA, let alone attacked it? Heck, we seldom bother to attack road convoys or barges, either (and those don't shoot back). My thinking is, how do you make them relevant? How do you make players want to attack them and defend them? Historically, attacks against transportation infrastructure such as bridges, rolling stock, rail yards, and locomotive and truck factories (collectively referred to as "the transportation option" in planning the Allied bombing campaign) were extremely effective (more so than the "POL option" of attacking energy targets).
I want to throw out a few ideas to stimulate discussion. First, how about the ability of players to spawn the convoys, like a supply run only on steroids, with man-able ack for defense? How about trains supply towns, and towns supply their attendant base with truck convoys? How about a factory for trains/trucks as part of strat? How about a major rail yard in each sector (attached to a base town, perhaps)? Just a few ideas to get the train rolling, so to speak.