Speed: There is a very narrow range of trip lengths for which high-speed rail makes sense.
Suppose this train actually achieves the stated 236 miles per hour. Without making any stops at all, you're still looking at about 13 hours to get from New York to San Francisco. With five or six stops (that's not even one per state), it would approach 20 hours. This is a 6-hour flight. Anywhere farther than 600 miles is going to be faster by air.
For trips less than 250 miles, it's just not worth the hassle of getting to a major rail hub, parking your car (or taking transit and transfering), waiting to board the train, arriving at your destination with no ground transport and having to rent a car, etc.. It's easier to just jump in your car and drive there. Cheaper, too.
Those are best-case scenarios. In reality, the Acela takes 8 hours to get from Boston to Washington, DC -- a flight I've made in about an hour and fifteen minutes.
Cost: Anyone with $50 or $100 million can start their own airline, leasing a few planes and plying low-volume routes to make money for expansion.
Good luck getting a high-speed rail built for less than $50 billion. With that kind of money, you could outright buy 40 or 50 brand-new airliners and hire people to fly them. That lets you provide service to a lot more than just two cities.
Capacity: It would take over a decade and untold billions of dollars to build a track. That's ignoring all the right-of-way and environmental headaches. Once built, the track can't exactly be picked up and moved if peoples' travel habits change. Air routes change all the time, based on passenger demand.
Airspace is already there, and it's free. The only real limit on capacity is landing slots, and big airports like LAX can land over a thousand flights a day.
Security: In flight, the only external threat to an airliner would be from ground-to-air missiles. Those aren't exactly easy to come by. You can't make one in your tool shed. Airliners are very delicate, but they're also very hard to reach, six miles above ground and moving along at mach 0.8..
High-speed rails travel a fixed route at predictable times. You could destroy one pretty easily using an IED. Even a small fuel-fertilizer bomb would be sufficient -- moving at hundreds of miles per hour, anything which gets the train slightly off-kilter is going to cause massive casualties. Patrolling thousands and thousands of miles of rail, 24 hours a day, is impractical and expensive.