The shortest SFO-LAX flight I see right now is 1h25m. Even if you made smaller, local, more efficient airports, I fail to see how you can hit 53 minutes while including commute time to the airport and clearing security.
You have to include that for the rail too, obviously.
Yes. You won't need to leave as much time for the train station as you do for the airport. Why? Because the airport services many more flights and is much more crowded. If we had more airports, it could become similar to a rail-station in terms of time needed at the station/airport.
In terms of time though, flying would still be faster, amazingly.
Flying: 45 mins to airport. 1 hr in airport. 1.5 hr flight. 45 mins to destination. Total: 4 hr
Rail: 45 mins to station. .5 hr in station. 2.75 hr travel. 45 mins to destination. Total: 4.75 hr
A rail line can easily move 20k people an hour, can't say the same about a similarly priced or staffed airport.
I can get to mine in <20 minutes on a bicycle.
2. Airport security. Add 15-45 minutes depending on density.
3. Delays. Frequent & much more common with airlines than trains. (add 1-several hours every hundred flights or so).
4. Capacity. Need 100 more passengers capacity? Add another carriage to the train or schedule an entirely different flight.
4. Also add in that you're wanting to cram in a bunch of airports into a few hundred miles of each other. You have to take into account that planes are moving at 550+ mph and need lots of clearance around each one. It's a lot easier to even schedule another train 10 minutes behind an existing one than it is to schedule another flight (considering the variables of destinations, companies and other logistics involved).
There's a reason why ATC jobs are some of the most stressful in the world. Flying seems easy, but the logistics behind it are intense.
And to boot: some of it is easy. You just have to bend one rail segment. Manually (which is doable with basic DIY equipment), or explosively. If you're okay with trying 5 times a large boulder positioned between the tracks where it can't be pushed aside easily has a decent chance of derailing a train. And that is a disaster. The amount of stored power in a train's movement is more than enough to destroy it. When this sort of shit happens by accident, there's usually double, sometimes triple digits dead. Targeted, you could do more. Without a few particular train lines, US oil production would slow to a crawl.
They are also far easier to destroy than to rebuild. Terror attack, and things go back to normal in a matter of hours. Sucks for the 5 people, but the economy is not going to be seriously impacted. With trains, and because there's a lot of cleanup, after which the entire line needs to be checked (and obviously not with a high speed train) a derailed train will take a week or two to fix, more on longer lines. It seems to me that disconnecting small cities in middle America from the train network and make coast-to-coast freight go a LOT slower wouldn't be out of the question for even a small organisation.