Because a big advantage to trains over airplanes is you can stop at places in between for low cost. It is common for airplanes to spend more time getting from the gate to cruising altitude and back down than at cruise.

A train going Chicago to Minneapolis would only lose a few minutes stopping at cities like Milwaukee WI and Madison WI - both fairly large cities. An airplane could stop at each, but the cost of one stop would double the full trip time.

Where a train stops vs go past is a very complex subject full of trade offs. However in general a train that only goes non-stop between two points is a bad idea. I've been in discussions elsewhere in this topic about that - read them for more info. (including those who disagree - they have valuable insight)

I guess I don't understand, you seem to be explaining why the non-stop aspect is a genuine benefit for trains.

They're explaining that cost-per-stop is much lower for a train than an airplane. A stop might cost an airplane an hour or more added to the duration of the full multi-stop route (slowing down, losing altitude, landing, taxiing, boarding, taxiing, take-off, gaining speed and climbing) even if we allow for some pretty serious optimization of processes. It might cost a train anywhere from 1-15 minutes. A train can make four stops between two points and, despite traveling at a much lower top speed, finish the whole route much faster than an airplane would, doing the same thing. That is, it's friendlier to multiple stops over medium-distance routes than an airplane. If you're going point-to-point and it's a very long distance, you may as well just take a plane. If you have a 250 mile route and want a stop every 50 miles, then a train's (way) better than an airplane. Multi-stop (not to be confused with excessive stops) routes are exactly where trains shine.

A HSR train stop and go - without opening the door is about 1.5 minutes added to the total trip time (depending on how fast the train goes of course). It is possible to get the time the doors remain open down to under a minute (this is done for airport trains), but I think 1.5 minutes is a more reasonable floor just because people need some time to get their bags on the train and around other people.

This puts the time loss to stopping a train at 3-17 minutes.

Sure, HSR is gonna have it worse than a minute, I was thinking of, say, subways and light commuter rail, with the 1 minute lower bound. Some of those don't spend more than about a minute not at full speed for some stations, including door-open time and de-/ac-cellerating. No train where people aren't traveling very light and prepared to get off fast is going to get quite that low a stop time, though, true.