We recently had a long discussion about the target choices on here; check it out. It discusses why Tokyo was not seen as an ideal target (in brief: it was already too bombed out by that point, and the goal was to get surrender, not kill the Emperor), why Hiroshima was chosen (military base surrounded by urban area = shows the power of the bomb plus is ostensibly military target), why other targets were chosen (Kyoto = nice big industrial target, but not military enough for Stimson; Kokura = same deal as Hiroshima), and how Nagasaki got appended to the list (other targets got destroyed previously; it was a very low-priority target compared to the others). You can also read the May 1945 Target Committee deliberations which is the best single document for understanding the mindset of the people who chose the targets (it does not include Nagasaki, because Nagasaki was at this point not considered a high priority target — it only made it to the list when Kyoto and Yokohama were removed, and on the day it was bombed it was the secondary target, after Kokura).