When possible, they pick "control points" at places where there are usually no passengers on board — for example, the ends of a linear route, or the bus depot.
But otherwise, they have a bunch of optimizations to spread the pauses out so they aren't too jarring. They also display the timer prominently so that riders are aware of what's going on.
In practice, riders seem happy with the tradeoff, since it has resulted in overall lower times to get from point A to point B.
This phenomenon is called "bus bunching". My friends, two profs from Georgia Tech and UChicago, came up with one solution for it. They wrote a paper about their solution[1], and then built a startup that has successfully implemented it at a bunch of places[2].
— Milan Kundera, The Book of Laughter and Forgetting