Many times governments will locate their industrial plants nearby a city so that the employees can easily get to and from work. There's very few ways to separate the people from the work that they do and with unsophisticated weapons of the WW2 era the more they bombed the better the chances they actually destroyd the industry. Another thing is pcychological warfare that makes the will of the people break by saturating bombing the entire area thereby breaking the "we can win" mentality from those who are willing to work for the war effort.
Fire bombing many of the major cities of Japan destroyed more than one A-bomb ever did but the psychological edge the A-bomb gave the allies was the edge they needed to bring about a swift end to the war with fewer allied losses. The fire bombings killed more civilians than both A-bombs ever did but that didn't bring the war to its end which was why they tried that at first. So whether or not an A-bomb should be used on civilians is going to happen by the country that either wants to win at any cost or the country that's losing the war and has nothing to lose. The question should be when it will be used not if it should be used in todays war torn world. Those in charge only want to get what they want and need no matter what the cost or who it costs.