Zarine and Unhostile, the cars are linked with citizens. Cars don't just appear out of nowhere, they have owners and the cars appear when they are used. Ypu could for example see a person leaving his house, walking to the street, and then the car appears and the person drives away. If there's parking space, they can leave the cars there, otherwise the car will just conviniently vanish when the person switches to walking or public transport. Every citizen does not own a car, it's calculated based on their social class, so business men and workers are more likely to have cars, whereas students and dropouts rarely own any.
As for the bunching up, there's currently no way to set a schedule. The way I do it is usually just have as many vehicles on a line as needed, since the passengers don't like to wait long. I'm currently trying out the Helsinki map and I have lots of long bus routes working fine when there's enough vehicles (up to 10 on the longest line). The scheduling would be a nice addition, but we've decided to concentrate on other issues, as the schedule is rarely a hard problem to solve in-game.