The bullet train is almost certainly faster than the flight when factoring in security, distance from the city center, etc.
And even if this ends up replacing all air travel between Tokyo and Nagoya, you're talking about 500 people each way per day. That's a fraction of 1 of the 33 bullet trains that already run between these 2 cities.
I don't disagree with this project. But it's evident that the project simply doesn't make sense in itself. It's clearly a Proof of Concept that Japan is using to be able to sell MagLev technology abroad in places which currently do not have existing high speed trains and will be choosing between paying a lot of money for bullet trains, or slightly more money for an even faster Maglev train.
Which is a significant justification IMO, but that's a very different justification from saying that this new MagLev line makes sense in of itself.