1. Eminent domain and generally-high construction costs make the initial time and money outlays exorbitantly high, resulting in projects never getting off the ground or having to compensate with much-too-expensive tickets
2. Even if you get to the middle of another city, having to rent a car to get to where you need is a pain. It's easier to drive from Dallas to Houston in a car, because you have a car at the end of the trip. Only some cities have fast public transport; the rest are so big it's hard not rent a car or Uber everywhere, both options are expensive and time-consuming.
3. Trains likely take more time than flights for the mid-to-long distance journeys planes are good for.
4. A cultural lack of interest in passenger rail. It's just not a part of the culture, and is seen as weird/enthusiast thing to do, unlike in Europe, India, or China.