The issue with coal, as I best understand it, is that for all the improvements (and there have been improvements), it's still pretty terrible. China, with their rapidly improving but still incredibly terrible pollution issue, is one example of what an unrestricted coal industry can do. Thus, environmentalists and others would very much like to gut the whole industry like a mutant fish, and since it is much less economically important (and just as polluting, if not moreso) than oil and natural gas, it's also an achievable and desirable target. So what? Well there are regions which depend on coal economically, and those regions (some already poor, like West Virginia) would be devastated (incidentally, if we tried the same thing with Oil, the exact same thing would happen to much more prosperous places like Texas). As such, there's a small but influential demographic of poor and blue-collar workers (and other people in those regions) highly opposed to coal restrictions and reductions, and this demographic is a thorn in the side of the Democratic party. Trump, of course, has denounced coal restrictions as job-killing and this fits with his blue-collar appeal.
It really comes back to arguments about how to revitalize regions with economic problems, except here those regions are not yet gutted, and thus have more political influence with which to defend themselves (while regions that are already suffering economically, like Detroit or parts of upstate NY for example, usually have little political power). So environmentalists and the coal industry butt heads and leave room for individuals like Trump.