I'm not sure I follow - if you are in a smaller city, chances are you live far from an airport, but still very close to a train station. Unless, of course, you fly private charters to minuscule landings.
Let's take, for instance, my hometown in Asturias, Spain. There's technically a train sttation... which will get someone to Madrid in about 8 hours. If someone wanted to go to Barcelona, the fastest route is still via Madrid! Going to Bilbao via the northern corridor by train is a whole 10 hours: The route is prohibitively expensive to tunnel for high speeds.
However, let's look at plane options. There's a single runway airport about an hour away with direct connections to Madrid, Barcelona, Las Palmas, Malaga, Valencia and Tenerife. Pre covid, it also had direct flights to Paris and London. The typical planes that land there aren't private jets, but just the typical narrow bodies that do short routes everywhere in the world: A319 or so.
So yes, there absolutely are plenty of cities in Europe where the train doesn't even begin to be competitive, in either price nor travel time.
Well, and that's about it. I don't care for Paris that much, there are about thousand other places I prefer visiting. Its not that exotic to Europeans compared to Americans, and Paris' painful and obvious drawbacks (its a mega tourist trap, rampant crime, french are often rude if you don't speak perfect parisian french etc.) remove a lot of its allure.
Currently we travel to nearby islands with small kids (balearic, canarias, sardinia, corsica, greek ones etc.). We travel home which is 1500km away (1:30 flight to +-nearby airport, or 15h+ multi-train galore), we travel exotic (0 options for trains).
Heck, being Swiss, we use practically 0 Swiss trains. They are super expensive even for us since we don't commute by them to work every day, and Geneva being border town literally at the edge of confederation surrounded by France has little use of rails for us. France has pretty bad rail situation in comparison - our usual way to Chamonix takes 45mins by car, and 2+h by train. Family of 4 with 2 tiny kids? Never, ever, with all necessary luggage, even for free.
You can't have cheap good reliable railway network even in dense Europe, unless its heavily subsidized. Its a pipe dream, nice one but unless they tax flights into oblivion they will remain as easier and cheaper option for most. Options will be different for rural living and different family settings obviously.
I guess you know that, but if you live in Switzerland you're supposed to have the discount card ("demi-tarif") which makes the train way more affordable. It's still not cheap, especially if you compare with a car trip not taking the price of the car and maintenance into account (which is reasonable if you need the car for other reasons anyway). But in my case at least, without kids, it's really worth being able to use my time to do something productive rather than driving.
Also curious about the Chamonix example: I've never lived in Geneva, but aren't there a ton of other options in Switzerland that are way more connected than the French side? Why choose this example over Swiss resorts?
Besides there are pretty places much closer in France. France is also much cheaper, food better. Not that many reasons to chose otherwise for short weekend trips.
Car is unfortunately a must for family of us, any alternative is world of pain and limitation, even ignoring the prices of trains (just like any other family we know). You need so much equipment for whole family and small kids especially, that using trains means we wouldn't be traveling at all. People we know that don't own the car rent it out every weekend they need and waste tons of time and energy on chasing lower prices. Even with demi-tarif/halb-tax (which makes you waste 200 CHF/USD per head per year for no services), the prices of Swiss trains are properly bad. It still is marginally cheaper to take one's own car even if driving alone, and often much faster.
Frequent experience from times before when I was using Swiss trains for commute/traveling around - you end up standing for quite long amount of time during normal times, many people travel everywhere. Not nice if you are ie tired after long hike/skitour. With small kids, just a horrible experience.
All this ignoring current covid crisis and the fact that in trains here you are stuck in long narrow tube with 100 other people, few coughing, few sneezing, few not wearing masks on nose, or at all because they hold that can of beer for 2 hours to have an excuse, kids not wearing anything at all etc.
Of course if you work in Geneva that's a different matter. There aren't any trains in Geneva as it just isn't big enough, but unireso's tram network is widely used.
This is particularly timely because right now there's a hole in the line between Lausanne and Geneva. Consequently you can't currently take a train either way and have to use a replacement bus. The autoroute is seeing stupid levels of traffic right now as a result as all the people who usually take the train get in cars instead.
Chamonix is almost certainly slower by train unless there are traffic issues. This is also likely true of the Swiss resorts too because personal motorised transport avoids the inconveniences of waiting and changing that trains inevitably have. But the article is about eliminating short haul flights in Europe, not this.
By contrast, that's roughly the same price as an annual ticket between central London and a town about 30 miles away.
If you want to go with train from east Germany to Amsterdam you still have to go to Berlin. It still takes ~6.5hr of train ride from Berlin to Amsterdam. Where flight is ~1.5hr - of course getting through security and all it is at least 2.5hr and then depending on which side of Berlin you live transfer from your place to the airport. Which I would say does not matter because for train you still have to get to Berlin HbF. You might have direct connection to Berlin HbF but as well some people might have direct connection by bus or train to the airport.
Most trains/ICEs will stop at 2-3 stations in Berlin. Usually they stop at least at Spandau and Hauptbahnhof, and sometimes Gesundbrunnen as well. You should be able to reach one of these stations in at most thirty minutes regardless of where you start.
All of these stations are major transport hubs and thus easy to reach.
Airports not so much: It takes me more than 90 minutes to reach BER[1], meaning I should probably depart from home at least 180 minutes before takeoff if I want to catch my plane most of the time. Note that it is usually recommended to arrive at the airport two hours prior to takeoff (or even three hours for international flights).
Following all the best practices and accounting for delays in public transport would mean I'd have to depart almost four hours prior to takeoff for a domestic flight.
To catch an ICE I usually depart from home about 40 minutes before it leaves Gesundbrunnen, which gives me enough time to grab some sandwiches at a bakery and a coffee that doesn't suck (DB is clearly taking their inspiration from airline food).
Of course, one guy was prepared and literally _ran_ to the FEX. We walked and then waited 30 mins for the next one to arrive. :)