Having just been on-site at a couple of Australian coal mines, I can say that they take dust very seriously. They spray water regularly over the haul roads to keep it down, and get workers to wear dust monitors to monitor exposure.
However, there is a huge difference between the likely exposure when coal is being blasted/cut, dumped in trucks, and loaded into trains from conveyors, than any hazards from passing trains. Of course a port where coal is loaded needs to be careful of dust, both for the sake of their workers, and for their neighbours.
So, it's one of those scare stories that is a real risk blown out of all proportion. As if we didn't have enough of those already...
Paul