Example: From Amsterdam Airport to Palermo, there are 2 flights per week (Friday and Monday). That is 300 passengers per week. It is a profitable to fly planes between these two cities, but a direct rail route including maintenance of the railway system would be far to expensive. This is partly resolved by stops along the way, but definitely not completely. The busiest direct railway routes (AMS-PARIS, AMS-LONDON, PARIS LONDON) in Europe are far from full, with one train an hour.
So the problem is not insufficient capacity, but rather that the scale is to small. I see electric buses playing a big role in the future to allow for better point-to-point connections.
Much like the idea of separating ISPs from the last mile infrastructure by the way.
Timetabled connections are likewise impossible to set up with too much uncoordinated competition, because without making the connection times unattractively long they cannot really be set up between more than one train per relation (maybe sometimes two at a stretch).
Plus connections that aren't ridiculously padded (and therefore result in absolutely uncompetitive journey times) really only work with some sort of through-ticketing so passengers aren't left stranded if they do miss a connection after all.
In Europe. But not in the US.
https://www.freightwaves.com/news/railroad/us-and-european-f...
http://www.mapattacks.com/2015/01/who-owns-americas-rail-inf...