I sincerely doubt the jet in question was flying at supersonic speeds right above tree tops. Couple of reasons, at low altitude most military jets can only handle mach 1.2 or so at the cost of massive fuel consumption. Any sort of long distance flight at low altitude, supersonic speeds would waste massive amounts of fuel. Additionally all aircraft are significantly less maneuverable at supersonic speeds which is a bad combination with being close to the ground. Lastly and probably most importantly sonic booms are really really loud. As in they can at least in theory kill people if in close contact(not aware of this actually happening at any point, but there was a cold war project to use a low flying supersonic aircraft as an anti-tank weapon). Point is if they actually where supersonic I would be surprised if you didn't have some form of hearing damage. Also shaking and rattling is not consistent with a sonic boom, just normal jet noise.