I see some flags... does that mean Imperial model, or minor civs?
The flags in CCM are available for those civs by civspecific era-none techs. They are used as perequisites for civspecific buildings, especially Great Wonders, and give one culture.
To start a Golden Age, in CCM three special traits must be fullfilled by Great Wonders. Each Civ with a flag has it´s own GW, that triggers a Golden Age for that civ in a correct historical period. Comments from new CCM prebetatesters like:
"By the way, I got my Golden Age not long ago when I fittingly built the Brandenburger Tor in Berlin" are no surprise.

The ability to start a Golden Age by a victorious "unique unit" is removed in CCM. The option, to trigger a Golden Age by a civspecific wonder, if it wasn´t triggered before , in my eyes is much better.
These flags also ensure, as they are needed by other buildings as perequisites, that the Royal Navy can only be built by the Brits, the USAAF and US Cavalry by the US, Tankograd and the Kirov Factory by the Russians and so. These buildings mostly autoproduce some heavy or superheavy weapons that are added to the normal units that are produced by the AI. With this methode for example Germany in time of WW 2 not only has the normal PzKpfw III, but also some Tiger tanks for special breakthrough operations.
This is also the methode used in CCM to solve the riflemen/machinegunner/tank production problem for the AI. The AI would always tend to produce the machinegunners with the much better defensive value as the better defensive unit compared to the normal infantry and the AI also would tend to produce tanks as the better offensive unit compared to WW 2 infantry. Therefore too less normal infantry would be built, what is a nonsense in my eyes. So machinegunners are additionally autoproduced to have some stronger units for defensive focuses.
The flags also play an important role for the "all civs but one should autoproduce a special unit"-problem. This problem was triggered by the special WW2 unit sets from Firaxis for PTW, where often Germany had another unit than all other civs. In CCM there is still the German flamethrower for Germany and the US flamethrower for all other civs ( the same constellation with some other units).
This is the way, how CCM solves this problem:
Germany has a special small wonder, the German Military Academy, that uses the German flag as a perequisite so it can be placed on the techtree at the proper place. All other civs but Germany have the normal Military academy as a small wonder. This small wonder gets obsolete by a special era-none tech for Germany. So it is ensured that Germany can´t build both small wonders.
The German military academy now is the perequisite for another building that produces the German Combat engineer (or the Panzergrenadiers and so on), while the normal Military Academy is the perequisite for autoproducing normal combat engineers, motorized infantry and so for all other civs. This methode has the additional advantage that now these autoproducing buildings can go obsolete with the normal techtree, what wouldn´t be the cause for directly autoproducing buildings (like the normal military academy) as this building was yet set to go obsolete with a civspecific era-none tech.
The flags are also a first step into civspecific traits for every civ. As they are buildings, you can give a big mixture of advantages or disadvantages to every single civ with them.
Last but not least: It is fun to show the flag of the civ you are playing in the cities you are ruling.
