You can only save the monorail, if you go defuse the bomb before reporting to Hsu.
Indeed, this seems to be a glitch. It's very hard (but possible) to run right from Hsu to the monorail after he tells you to go save it and get on board and defuse the bomb. But no matter how you defuse the bomb or how long you wait, when you walk off the car it goes off and explodes. This is a bug, or at least I think so.
The only way to save the monorail that I've found is to listen to the entire spy conversation till your pip boy updates to save the monorail, kill the spy and grab the code and run for the monorail (knowing already where it is) and defuse the bomb. Then go to Hsu. That seems to work. Very frustrating defusing the bomb and still having the fricking car blow up just because I went to Hsu first.
They ought to fix this, but then the buggy freeze prone nature of the game would I think have top priority As a software developer, I understand how hard it is to fix bugs like game freezes and quest problems, but clearly somebody at Bethesda should have improved the freeze prone nature of the game by now. It's really a great game brought down by its bugginess.