I didn't want to fly – so I took a cargo ship from Germany to Canada

You will have to add some time to flying scenario. You have to arrive early to the airport to go through security (2 hours?), you have to wait for your luggage after landing (30 minutes?), and since airports are usually located outside of the city center you have to add travel time to and from the airport (45 minutes in each direction?). In my example that's an extra 4 hours added to the 2 hours time flying.

It's still a lot less than going by train, but with train you get the convenience of being able to run onto the platform 2 minutes before departure, you end up in the city center, you pick up your luggage and leave, and you usually have more space which makes it easier to work on the train if needed.

Also, flying is extremely subsidized and tax-exempt. I just read articles (in Swedish, so I don't know if anyone wants links) claiming that air tickets should be between 50% and 95% more expensive if they had to carry their own costs, if there was a tax on airplane fuel, and so on. So the price for air tickets probably doesn't reflect their real costs, and obviously doesn't take the environmental effect into account.

But even adding the extra time and extra cost, it would still be faster and cheaper to fly than to take the train, which is unfortunate from an environmental perspective. I wish we had faster trains, and a lot more overnight trains so that you could start your travel in the evening and wake up in a new city. It wouldn't help with a 40 hour trip, because it would still be two nights with one full day on the train.

This might work for people who can work remotely on the train, but not for everyone. Start you journey on Thursday night, work Friday on the train, and arrive Saturday morning at the destination. Someone I know did this recently while traveling to a conference, and the company obviously paid for the tickets. This doesn't help when visiting family, but for work travel, train could be an option.

I have an airplane interested colleague and I asked him about environmental fuels. He said that aviation biofuel already exists, and it's just a question of adoption and scale. A carbon dioxide tax might push air companies towards biofuel, or you could have the option of green biofuel departures and let the customers decide if they think it's worth the extra cost. I'm sure my train-traveling conference goer would consider that option if it was available.

As I said, I agree with your main point that if you just look at price and travel time today, the less environmentally friendly option makes more sense. It would make more sense if the slower option was also much, much cheaper than flying, because that would encourage more people to use that option.