When in Kenya, I tend to try to live Kenyan. I am there on a budget so I am not going to hire a car, and the only car I did have the use of was destroyed during last year's PEV.
So, it is public transport for me, usually matatu or shuttle, or coach, when going to the coast (because going to the coast is 'holiday').
Matatus and CitiBuses are fine to get from the suburbs into town. Mataus are 14 seater minibuses that run a specific route which is displayed by a hand-painted number badge in the windscreen. This is fine as long as you know where the routes go, not so good if you don't. You can always ask a tout. They are usually very helpful.
On a short matatu journey, it does not matter too much where you sit. Every seat is uncomfortable and these vehicles are usually packed with people and luggage, which can include livestock.
For longer journeys, there are the shuttles. These are 12-seaters and provide a non-stop service between far-flung towns, stopping only for a refreshment break.
When using shuttles, there are a few points I would make.
Firstly, there is fierce competition for your custom. Touts will guide you to their vehicle. Don't be bullied. At the very least, check the tyres and if possible, get a general idea of the state of the vehicle.
Shuttles do not leave until all seats have been filled. Having found one in reasonable condition, try to get a seat between the axles. The back seat is to be avoided at all costs, unless you like being bounced between the seat and the roof of the vehicle. Personally, I like second or third row, right window seat. If you are brave, you could sit up front, next to the driver. But in a head-on crash, front seat passengers are the first things that get hit. Avoid the seat over the engine. Six hours on that will cook your butt!
When travelling by matatu or shuttle, remember that fares are the premium for the driver and tout, and more journeys mean more fares. So they get to wher ethey are going to as quickly as possible - they have two speeds, stop and full speed.
And to give you an idea, I was once in a matatu during a driver change-over. The driver got out while the vehicle was still running and the new driver jumped in to take over. We lost about 3 seconds on the journey!
Also, don't be surprised if the vehicle breaks down en route. But don't worry. The tout will climb under the bus and usually get it going again.