why a train journey from San Francisco to Los Angeles has to be 12 hours long

That's its own saga, with a bunch of factors specific to California politics (and national politics with funding and permitting California projects). The California High Speed Rail project intends to connect SF to LA in less than 3 hours (and the original 2008 plan aimed for a 2020 operational start date), but we'll see if that ever comes to fruition.

Also, I guess you guys do not regularly travel from New York to Los Angeles for a weekend trip, just as we Europeans don't usually do that with Stockholm and Barcelona (which is a distance the average European would also travel by plane).

One wrinkle in comparing things is that the US's cultural affinity is less tied to geographical proximity than in Europe. Obviously European villages and cities and major population centers were established long before rail, much less before automobile highways and commercial air travel (or even before global television broadcasts), so each local region will have its own culture and language.

In the U.S., with the population centers built up much more recently, cultural affinity between cities or regions is distinct from geographical proximity. So for many, a weekend getaway or a one-week vacation will tend to look to other similarly sized cities. One joke in the TV show 30 Rock was the idea that someone from New York would want to move to, or even visit, Cleveland. This is especially true for those who aren't straight white Christians, where much of the geographical footprint of the United States represents urban islands where you might feel like you belong, and where you'd want to hop from island to island rather than explore the vast areas geographically nearby.