I don't see any reason to believe that all the machines were necessarily buried underneath major cities. Many may just as well have been somewhere out in the boondocks. What difference would it make? They could travel pretty fast.

It was an odd idea to have the machines buried, since in the original story there were spacecraft that arrived as projectiles, and gradually opened themselves. That made for a spooky and suspenseful opening scene of the Martians in the book. I guess Spielberg decided against that, because we are too familiar with spacecraft now, and the military would have reacted immediately to such landings. He had to come up with a new surprise angle of some kind for the modern setting.