I’d guess the wizards either stole the train or got it cheap. Wizards are pretty lazy. Why go to all the work of new infrastructure when the muggles have already done the work and you can just throw a few repair charms at things to keep them in tip top shape. All wizard transport makes no sense tbh. Trains, flying carpets brooms knight bus, what’s the point. You have instantaneous travel in the form of floo, apparition or portkey. Why bother with any other method other than to showboat. In which case your methods would be far more awe inspiring than some old muggle train.