A few facts to help out with your perceptions:
The emissions from automobiles really do not go up into the upper atmosphere. They tend to stay in the troposphere, which is the part of the atmosphere that's closest to the surface, and the majority are washed out by rainfall. They don't harm the ozone layer. That's caused largely by chlorine-containing pollutants.
The largest particles from coal do indeed settle out much closer to the point of emissions than do those from autos. But oil emissions tend to be quite small in size, and can be carried quite a ways. The biggest issue with size isn't so much how far they go - the farther they travel, the more air they tend to be associated with, and therefore have lower and usually less harmful concentrations. The major issue is how far into the airway they can get, and smaller particles tend to penetrate much deeper.
Yes, indeed, any sort of combustion system pollutes. But you have to balance lots of variables when you consider health risks associated with pollution. A very high concentration in a coal plume can be worse than the much smaller concentrations in urban settings, even though you're exposed for a short time to the high concentration and for a long time to the lower concentration.
Pollution can be a very emotional issue - but also a very serious one. Like the gentleman said in the Ely article, it's a matter of deciding which emissions we choose to accept. We should do that based on facts, not emotions.
Andy