I think there are pros and cons to both structures. Villages in Switzerland are well separated by geography that is physically difficult to overcome (i.e. mountains), even if the distances are not big. It's way easier to lay down a flat, long rail between 2 cities in, say, the US or Mexico than it is to do the same in Switzerland.

The structure would probably need to change for larger countries though, it's true. But you could keep a lot of it; create long distance rails between major cities with stops along these rails for smaller towns to feed into. Some European countries have this type of structure, Italy for example, though it does get very tricky for the very smallest villages