Considering city centre to city centre is only relevant if you're travelling from a city centre to a city centre.
Quite. I go to Geneva at least once a year, and need to be there early as possible. If I take the first available train option, I need to leave home at 0430, taxi then train to St P, and I get to central Geneva at 1430ish.
If I take the plane, I leave home at exactly the same time, and get to Central Geneva by 0930. And the plane is usually substantially cheaper, even given that I get the train at staff rates.
Even with the quickest train option, using the plane is about 3 hours quicker. Given that the train cannot compete on price for this distance, it's only real market is going to be for people who won't fly, those who will find the train journey more productive work wise than the extra time at each end, or those who just fancy a rail trip.