it's difficult to separate all the channels in a car that way. ECUs require a good amount of protection from vibration, shock, heat, and cold. If you ever look at an ECU box it isn't exactly tiny. There's no getting around that. So simply installing more boxes isn't exactly an option. It's not like an iphone that you just carry around in your pocket so it won't get damaged unless you drop it like a bumbling baboon.
There's only so much wiring that can plug into an ECU, and it has to be able to interface with OBD-II on a hard connection for emissions testing still, although there are companies nowadays like BMW that have the ability to remotely connect to a car's ECU for diagnostics and coding and I'm sure one day soon emissions centers will have similar tech available for modern cars equipped with technology packages. But right now it's all proprietary. Either way, separating it all out is a lot of logistics, wiring, and circuitry. And at the end of the day, it can all still be hacked. Even if a manufacturer were to create (conceptually) separate "ports" for different channels of input, and locked certain ones down so only proprietary technology that the manufacturer owns could get in, someone will eventually be able to hack it.
There is also a logistical challenge there of what exactly to separate. IF you separate out media/speakers connectivity, what happens when you crash and BMW emergency calls your car? Today you get a call instantly from BMW to provide assistance or 911 calls, etc. But how does the car know it's been in an impact like that? Is it tied to airbags going off somehow? And if it is, how do you bridge that gap if you've separated vehicle communication features from airbag communication? What about any emergency shutoff switches in the car? If my car has iDrive which has integrated systems in the navigation head unit, how do you separate the features that impact driving, safety notifications, safety controls, etc. from media and nav?
These things aren't insurmountable but they require a lot of engineering. It's infinitely easier to have a single control unit that can tie everything together in the same spot, and then just secure it. Reliability/consistency of today's automated systems in cars is pretty critical and need rigorous testing. The quality assurance that has to be built into a process to develop that kind of isolation of features would be...staggering.
