Won't sonic booms prevent Space X's BFR intercity transport plan from being acceptable?
The only way to get anything that far that quickly is to send it into space, and that's exactly what Musk is suggesting. The BFR will launch a passenger carrying spacecraft out of the atmosphere and into a sub-orbital path, it will re-enter the atmosphere close to its destination. Rockets launch pretty much straight up and a sonic boom would have to compete with the rocket itself on noise. Once above the atmosphere there is no sonic boom because there is no air. 

On re-entry all spacecraft create a sonic boom, for most of the re-entry this is  inaudible from the ground because the air is extremely thin, once in the lower atmosphere it gets louder. By the time the spacecraft gets low enough to create a really big sonic boom it's usually at a subsonic speed and would not make any boom at all. The shuttle and Apollo spacecraft both created sonic booms on re-entry, that's covered in this Space SE Question. 

So, are sonic booms a problem in this idea? It depends, the space shuttle re-entered over the continental US many times and it never bothered anyone, but if it was happening a few times a day it might be a problem. You could get around that for the most part by re-entering over sparsely populated areas or the ocean. 

More likely it's not the sonic booms that people won't want from a noise perspective, but the launches.