None of the disadvantages you cite are intrinsically related to flying. We don't have to build huge railways, just remove the arbitrary barriers that make air travel suck. The biggest one being the ridiculous security theatre that is the TSA.

Commercial flight, even with the risk of terrorism, is far safer than land travel. If it's acceptable to let people board the Acela without going through body scanners, then there's no reason we can't do the same with JetBlue.