If you look at the online game and check the traffic congestion, you will see that some cities have absolutely no traffic at all, whilst other cities are absolutely full of private cars.
Being connected to other cities by road or not and city size does not seem to affect which cities get either treatment.
Although, disconnected cities that generate more city cars are even more likely to be full of cars.
Yeah, I've noticed this as well. Originally I thought that maybe the city cars just seemed to migrate to certain cities by the way the road network was designed but there are cities that are completely isolated from interconnecting roads that are just full of city cars and others that aren't.
Compare Reddley @6590,930, which is an isolated (no roads out) city:
(http://www.ssgholdings.ca/simutrans/images/reddley.png)
With Pelton/Charinglow @5680,400, which is two towns isolated on an island:
(http://www.ssgholdings.ca/simutrans/images/pelton.png)
Reddley is completely filled with private cars and Pelton has just a few.
I have changed the private car generation system for the next minor release to something that will hopefully produce more realistic results.