Where is this 'cheap' Air Raft of which you speak?
The problem of prices and the lack of economy in Traveller is something I think anyone who's played the game is well-aware of, right down to the inconsistent pricing and the lack of effects of the economies-of-scale. I don't expect them to have gotten it perfect; they were writing a game, not an economics textbook. But when a question is something like "would they have trains?" like the OP asked, I think factors such as economics do need to be taken into account.
It's my belief that given how effective and useful contra-grav would be and the way it is used in Traveller, should be a lot cheaper than it is; it seems unlikely that you'd have CG lifters on every tramp freighter, grav tank, grav APC, lighter, and gig (those uses alone, even if military, would create a massive demand and corresponding economies-of-scale). Factor in that CG technology has been in use for millennia in the TU (since the Ziru Sirkaa), and the price of grav seems suspiciously high (at least to me). Contra-grav is not like modern aircraft engines which only have a few applications (though it can be argued that the economies of scale for turbine technology, also used in aircraft have allowed turbine-based applications to be used in a modern home, even if the turbine isn't running a propulsion system) - it's more like the wheel or at worst something like an electric motor; it's useful for everything. Even in Traveller, they do use them for robots, cargo loaders, and similar things.
Contra-grav would have a much higher initial investment in the mover itself, but the rest of the set-up and continuing investment is likely cheaper. With things like railways, it can cost upwards of a $1 million US per mile of track, average with many projects costing more per mile. A lot more, like double, triple, even more per mile, just to set it up (just 30 miles of track, that's a lot of those Air/Rafts you could buy instead even at Traveller MSRP). Then you add in the recurring cost of upkeep of the tracks, the missed opportunity cost from land that the lines take up, upkeep of bridges and tunnels, and so on is a significant cost. It's relatively cheap if the train is intended for passenger or only light freight in an area where conditions are stable, but heavy freight or storms or similar situations will make upkeep significant. Again, a lot of colony worlds are likely to use anti-gravity as a transport system because the costs of setting up track are prohibitive (even if it is cheaper than the modern US because a colony world probably won't have to pay for right-of-way which is a large percentage of the earlier quoted per-mile costs); even later when they're more wealthy they understand that a ground train system might be cheaper in the long run some situations, the upfront cost is going to be big turn-off. (I'm also not sure there'd be a long-term savings, though.)
A "sky train" (contra-grav) in contrast might still have to pay things like a kind of "virtual" right of way tax to keep traffic and other hazards out of its route, but it doesn't have to pay a recurring cost its physical ground support structure that it needs to function. Upgrades and repairs must made to the "train" itself, but that has something in common ground trains. The strangely expensive Traveller computers only need to be installed on the controller car - the other cargo modules don't need them. A sky-train or sky-bus is likely to be pretty economical; but I don't believe it is the kind of train that OP was referring to.
Devices and technology in Traveller seem to last a very long time; they're ridiculously durable (from examples I was able to glean from sources like T4) and given the slow pace of technological advancement that suggests that a given device may remain in service for many decades on end. This would benefit all devices, but if a grav vehicle and a ground train remain in service long enough, at some point, I think they should converge.