Let's see if I can put this in an analogy you can understand...
Think about a gearbox. Every gearbox is about the same design, bunch of gears driven by an input shaft, driving an output shaft, selected by some sort of selector fork.
But there are also tons of differences, bellhousing bolt pattern, output bolt pattern, spline count on input and output shafts, ...
This is very comparable to the CAN-bus system used in modern vehicles. The standardised protocol describes how to send a message (basic workings of your gearbox), but not what's in the message (spline count of your in- and output shaft).
Now, wouldn't your life be much easier if all that was standardised and every gearbox could be used in place of another?