Why were Hiroshima and Nagasaki targeted rather than, say, Tokyo?

Because Tokyo was already obliterated by dozen of fire raids that left over more than 140,000 civilian dead in total (an estimated 100,000 were killed on March 9-10, 1945, which exceeded the civilian death toll than both Hiroshima and Nagasaki combined). And your premise is wrong, Tokyo had the highest civilian population (about a million) than Hiroshima and Nagasaki. Hiroshima and Nagasaki were mainly chosen because they had lower level of civilian population (less than 400,000) and contained key combatant and industrial targets. Just to let you know, "military" doesn't equal to "combatants" because military personnel can either be prisoners of war or belong to a neutral nation not at war or not in a warzone with a non-state actor. But the Japanese soldiers were combatants because we were at war with them.

Actually, Nagasaki wasn't supposed to be the primary target for the second bomb, it was supposed to be Kokura but the bad weather prevented it from being bombed so the bomber drove straight towards Nagasaki instead.

There were many reasons, but I think the most important from our present perspective is: someone had to be left to surrender. Even once the emperor announced surrender, it was difficult to convince some field commanders that the war was really over. If a-bombing Tokyo left Japan headless, units which were already sworn to fight to the death, would have to have been engaged one by one, which was exactly what the bombing was meant to prevent.

At the time, the places chosen were centers of areas that the US planned to invade -- if an invasion became necessary (actually Nagasaki was a secondary target because the primary target that day was overcast). So if the bombs had not ended the war, they would have at least softened up areas for an invasion.

Both cities had a military manufacturing presence. The city of Kokura was to be bombed but inclement weather saved them. Hiroshima had troops and military facilities and was a valid target. Nagasaki was a major seaport as well as having a large military contingent.

The reason why an atomic bomb wasn't used on Tokyo is because it wouldn't be very dramatic to drop one on a city that was already mostly rubble from conventional bombing raids. They wanted cities that had been as yet untouched.