I understand the idea that industrial centres were targets to cripple the enemies economy and military targets were obviously targeted to prevent any meaningful counter-attack. But why were so many targets population centres?
There are two basic strategies when it comes to strategic nuclear warfare: counter-force and counter-value.
Counter-force aims to destroy the enemy's ability to carry out a nuclear strike or nuclear retaliation. Here, you target missile silos, airfields and harbors where nuclear missile subs are. To defend against a counter-force strike you disperse your nuclear assets by sending your bombers to distant airfields and keeping your subs at sea. Missile silos are kinda hard to move around (although both sides had extensive schemes to move missiles around by train and by truck, with the Soviets working a lot harder in that direction), so they are instead hardened by burying them deep into the ground. This obviously means that the number of targets an attacker has to hit for a counter-force strike to work goes up dramatically - any runway long enough for a heavy bomber to take of from must be hit to be sure you get all of them (and a lot of them just happen to be international airports near major cities - oh well). Missile silos need to be hit with multiple warheads to ensure they destroyed. No one ever figured out quite how to counter-force strike subs with enough certainty (they work very hard to hide and have other subs protecting them).
Counter-value aims to keep the enemy from attacking in the first place by planning to destroy what the enemy values the most. Population centers are obviously very high on the list. This approach is very attractive because you can get it done with fairly few warheads. You just need enough to make any (nuclear) attack on you not worth it. The question becomes just how many cities the other guy is willing to sacrifice if that means he can utterly annihilate you. That's the point when you start to look at your intelligence reports about the latest numbers of enemy warheads and start to wonder just where those are supposed to be going, so you order up a few more just so the other side knows you can hit even more cities than he can.
And of course, more warheads are inherently more survivable (more missile silos, more subs to hide, more bombers on more airfields) in case the other side wants to try a counter-force strike. And if you have those warheads, you may as well decide on a target for them ahead of time since the last thing you want to do when the first wave of nukes is already flying is to go pull out a map of Russia/the US and start to ponder where to put those nukes.
Beyond that, you have the tactical/operational use of nukes. Here you use nukes to achieve an effect on the battlefield. These are aimed at high-value targets such as military airfields, command centers - and things like railyards, major highways and bridges. A lot of these are in or near major population centers.