The Windy City Flyer concept was actually a train I was thinking of creating and operating myself as a private venture. It took about 15 minutes researching the cost of running a train like that to nix the idea of doing it, as I could never capitalize such a project, and I'd have a hard time making a profit for it.
The route, however, eliminates a lot of your arguments. The route would run 945 miles. It could maintain a speed of close to 100 mph for the first 195 miles to Harrisburg, which it would accomplish in two hours. For the remaining 750 miles, it can run a speed of 70 mph on average. If doing so, it could make the trip in about 11 hours. Now, assuming we add another hour in there for a crew/engine change at Harrisburg as well as delays, the train could reach Chicago in 14 hours.
If the train leaves New York Penn at 6:00 (giving the average business man the chance to leave work and spend an hour getting to the station) it would arrive in Chicago the next morning at 8AM, giving the average business man an hour to get to a business meeting. The businessman enjoys a meal, a night cap, and goes to bed. He wakes up the next morning at 6:30, eats breakfast, and departs the train.
To one perspective, he's used up 14 hours of his life as opposed to two and a half. But lets modify that, because its inaccurate. First of all, that businessman would have to take 30 to 60 minutes to get to one of the New York airports, from his office. He needs to arrive there perhaps 2 hours before the flight leaves.
With the stricter baggage policy of airlines, it is more likely he will need to check baggage. If he does so, he can expect to wait another hour getting his bag. Now he needs to spend another 30-60 minutes getting from the airport to the meeting. So in reality, the flight takes between five and a half and seven and a half hours out of the man's life.
Second, the time taken out of his life on that plane, assuming he leaves the morning of the meeting, is from the hours of 4 in the morning (who wants to get up that early? O_O) and 8:30, assuming best times. If he leaves the night before, the hours taken out of his life are between 5:00 and 9:30 at best, 5:00 and 11:30 at worst. He then gets to spend money on a hotel room in Chicago, sleeps the night there, and is back where we started. He is not going to do anything useful between 9:30 and going to bed, he is not going to do anything useful between the time he wakes up and the meeting.
After the meeting, he can take the plane again. It will take him at least an hour to get from downtown Chicago to O'Hare in traffic. He can then fly home on an 8:30 flight, arriving in New York at about 11:00. He then has to once again get his bags, and travel home. He will arrive home at best at 1:00 in the morning and fall straight asleep. He most likely won't be up before 9:00. Alternatively, he decides not to get home at that ungodly hour, and sleeps over again. He can fly out really early to get home by 9:00, again, but it means he will need get up at 4:00 AM once again. A more reasonable time gets him home around noon.
Alternatively, he can take the Windy City Flyer. He once again leaves his office at 5:00. He boards the train at 6:00, checks into his room, and heads to the dining car. He eats a meal, has a night cap, and goes to bed. He wakes up again at 6:30 and eats breakfast, disembarking at 8:00. He gets to the meeting, and goes about his business. He leaves again at 5:00, boards the 6:00 train, and leaves. Eats dinner, has his night cap, sleeps, eats breakfast, gets off the train, and is home around 9:00.
He can do it in less time on a plane, sure. It means he has to get up at 4:00 in the morning, or earlier, and it means he has to get home at 1:00 in the morning. It is inconvenient, uncomfortable, and a lot of people wouldn't do it. He can do it in a similar time on a plane, with less of the getting up at 4 in the morning. To do so with comfort and convenience of not getting up at ridiculous hours, nor getting home at them, it will take him about 3 hours more, and he is still arriving in Chicago late at night.
In sum, the train is not as time inefficient as it at first seems.