Tokyo had already been heavily bombed. Hiroshima had suffered a lesser scale of bombing and was also not as well defended. There was some question of wanting to see exactly how much damage the bomb could do, so a relatively undamaged Hiroshima could give good results on the amount of damage an A-Bomb could do.

There was the plausibility of actually trying to target some military facilities and it was also a significant enough of a site to do some damage, kill a lot of people, and send a message that the war was about to get really grim for Japan. They might have dropped it out in Tokyo Bay or in a lower/underpopulated area, but they didn't have a very large supply of bombs, so there was also a need to do some significant damage with the ones they dropped.

Over a hundred cities had been firebombed by then, including Tokyo multiple times (see Bombing Civilians: A Twentieth Century History; Tanaka and Young). The largest cities in Japan were already mostly destroyed. Hiroshima and Nagasaki were both on a list of candidates that were likely to not be targeted in the 1945 firebombing campaign; this would allow warplanners to see how effective the new bombs were.

Dropping an atom bomb on the burnt out remains of Tokyo may not have been as impressive as destroying a mostly untouched city (and General Hap Arnold went ahead and firebombed Tokyo one last time after the A-bombs and before the official surrender; multiple sources including a Laurence M. Vance article).

A follow-up question. I've heard that Kyoto was supposed to be A-bombed originally, but one of the US generals who'd been there before vetoed that decision. Is this true?