The idea that large population centers would be attacked is completely plausible. In the articulation of your question I feel that you have too narrowly viewed strategic attacks. Yes Moscow and Washington D.C. would be primary targets, but so too would many of the major cities within the US and the USSR. The US and the USSR would at first attempt to take out each other's capability to perform Atomic Attacks. But, attacking a city like Chicago, or Boston, of New York would cripple the United States directly, and Cripple it's military indirectly.

First and Foremost these major cities are huge economic centers, the destruction of such large source of economic stimulation would weaken the economy. This would cause the standard of living for the common citizen to lower, and would also weaken the government's capability to build up resource that would be necessary during a War. Such attacks would also inspire fear throughout the countries population which could sway the general consensus to want to sign a treaty(even an incredibly one sided treaty) instead of taking part in a war that could result in the deaths of millions of people.

There is a primary source document entitled "Estimate of the Effects of the Soviet Possession of the Atomic Bomb upon the Security of the United States and the Probabilities of Direct Soviet Military Action" which deals with these ideas directly. Published in April, 1950 it argues that a successful attack including 200 hiroshima capacity bombs would cripple the American military and economy, and reduce the National morale so terribly that the United States would not be able to embark on an offensive war.

Think of a nations ability to defend itself similar to a human beings ability to fight off infection. While the Military is much like a human's immune system, the economy is the blood of a nation. If it is reduced too much the nation will be too weak to survive.

Ive studied this quite a it and many of my sources come from "Weapons of Mass Destruction" (ill add in an author tomorrow when i get back from holiday, cannot for the life of me remember the name).

Basically in the event of a Nuclear War there was 1 outcome and that was MAD or Mutually Assured Destruction. Basically the thinking went that if my country was to be utterly destroyed then so would yours, keep in mind that by the 1980s the USSR and the USA (with their allies) had enough nuclear warheads to hit each major city, town and village with multiple warheads several times that of the Hiroshima bomb.

The reason they would attack civilian centers is 2-fold, each major city will have an infrastructure network that will provide aid in the case of a war i.e. communications and having just 1 big radio up can rally the population, so all have to go. And the second reason is that each major city will have a military presence whether it be an airfield, garrison or a depot, so its best to hit every city to ensure a counter-attack will be implausible due to complete destruction of infrastructure and the military forces themselves.

On an ideological standpoint however it basically boiled down to "Do you want to live in a communist/capitalist world?", which often resulted in a "no". So the warheads would ensure the destruction of all enemy population centers to ensure that the opposing ideology could not survive the war.

Also i believe Metro took its inspiration off old war documents that detailed each and every nuke target during the cold war to be hit by nuclear subs, silos and mobile launchers. These targets basically covered the entire world with multiple nukes aimed at the Netherlands "because they are anti-nuclear" (Russian humor?).

These targets also included friendly territories i.e. the satellite states. The reason the friendlies would be targeted was as mentioned above an ideological issue, since the people in charge didnt want their enemies "winning" as it were. Both America and Russia had in place a system by which in the advent of a nuclear war the entire nuclear arsenal would be launched at both their allies and enemies respectively. The American system included the "Football" a suitcase with the launch sequences of most of America's nukes to be launched automatically should the suitcase go offline for a set period of time. Russia had a system where if a member of the Kremlin would need to put in a code every 30 minutes or else the warheads would launch.

So to basically answer your question, yes every population center period would be hit by a nuke in the advent of a nuclear war, even people in countries like Switzerland, the Netherlands, Madagascar etc since the mind set was "if my civilization ends, so does everyone else's".