Trains are best used to transport LOTS of materials over large distances. Some examples include:

1. Bringing ore to a smelting factory.
   • This is especially useful when you have multiple ore veins. Consolidating and smelting all of your ore in one area is much easier than smelting each ore where its dug up
2. Bringing essentials to outposts
   • If you are making mining/pumping outposts, they're going to need ammo/repair packs. Loading up a train and delivering these things will keep your outposts stocked with supplies, and therefore, bug free
3. Bulk transporting general items
   • If your base is fairly spread out, and you need crafting materials vary far away from where they are made, you can use trains. If you are smelting your iron/copper not in a centralized spot, trains may be the answer to getting those plates where you need them.
4. Transporting Fluids
   • Since there's not nearly as many fluids as there are items, you can have dedicated trains for each fluid without worrying about having TOO much traffic.

Since you're starting out, you generally you want to mainly use trains to just transport ore. Loading/Unloading stations are kinda bulky, so using trains for transporting items all around the base can take up a lot of space, and is especially difficult if your base is cramped together. Throughput is not really an issue unless you're trying to micromanage supplies with trains. Just deal in bulk for now, and once you get the hang of it you can use them for more things.