A high-profile, high-speed train in the U.S. would be believed to be a target for terrorists, so you'd soon find TSA going thru your luggage, just like st the airport.
Most countries don't do that though. Even China only x-rays your luggage. No need for shoes or body scan. A high speed train is simply much more resilient than an aircraft against small explosives.
Since the High-Speed line will only have one station in each city, you'll likely not live close enough to walk to the station, so now there's parking, car service, taxis, buses, etc to contend with.
In this respect it's similar to the airport, except that most people are significantly closer to the city center than they are to the airport. Of course the other half of the problem is that the US is seriously lacking in intra-city public transport as well. In Tokyo, you could take a 10 minute subway ride to the train station. The airport, on the other hand, is almost an hour away.
And I'm almost certain the passenger rail service would not be sufficient to justify running trains every 15 minutes, so you'll be waiting around for the train.
You only need to wait around for the train if you didn't bother buying the ticket beforehand. If you did, you could show up 15 minutes before departure.
With commercial flights, if you tried showing up without a ticket, you would be denied entry completely. If you try to buy it right outside the airport, you're going to wait half a day if not several days for a flight. And this is if you are willing to pay out exorbitant prices for a last minute ticket.