The main difference is that car companies perceive this type of open source tuning and tinkering of their product as good for business. In its best form, these aftermarket "car hackers" end up doing a better job than the factory, and the company hires them for their expertise (Shelby is the obvious example here).
The same thing happening in the computer industry isn't that unheard of. Lots of companies hire "computer security researchers" to look for weaknesses in websites, software, whatever. Most of the time, companies look at people messing with their devices with a sort of cautious indifference. Just like a car company looking at the unauthorized aftermarket for their products, electronics co's will say "these parts can seriously damage your device and we would never support their use." But they accept that they exist and go on with their life.
What Sony is doing, however, really is exactly the same as saying, "you chipped your car and can now run programs we didn't authorize, so we are going to take your car, sue you, and try to get you put in jail". If Sony wins, this could easily start happening with cars, at least with their electronic controls/ecu's.
I sincerely hope that with the courts increasing acceptance of "jailbroken" computer devices (linky) will keep suits like Sony's and, god forbid, any car company at bay.