The cities were chosen because they had been relatively untouched during the war. The Target Committee wanted the first bomb to be "sufficiently spectacular for the importance of the weapon to be internationally recognized when publicity on it was released."
In Dresden, from a British site:
My father was one of the "anonymous RAF meteorological officers (who) finally sealed Dresden's fate".
Normally, crews were given a strategic aiming point - anything from a major factory in the middle of nowhere to a small but significant railway junction within a built-up area. The smaller the aiming point and the heavier the concentration of housing around it, the greater would be the civilian casualties - but given that the strike was at a strategic aiming point those casualties could be justified.
Only at the Dresden briefing, my father told me, were the crews given no strategic aiming point. They were simply told that anywhere within the built-up area of the city would serve.
He felt that Dresden and its civilian population had been the prime target of the raid and that its destruction and their deaths served no strategic purpose, even in the widest terms; that this was a significant departure from accepting civilian deaths as a regrettable but inevitable consequence of the bomber war; and that he had been complicit in what was, at best, a very dubious operation.
The people who introduced the notion of targetign entire cities were Charles Portal of the British Air Staff and Air Marshall Arthur Harris. Others, from Churchill down went along with some reluctance (see the entire page cited above).
The justifications, such as those we've seen here, come from the eye-for-an-eye moral philosophy, incompatible with Christianity.