Uplinker, the difference is auto manufactures make them by the millions. Aviation makes them by the thousands - so massive economies of scale come into play. And that automotive engine that started at +40 C doesn't see minus 40C an hour later - aircraft engines do (granted, not as dramatic on piston engines as on jets, but still dramatic temp changes). That rapid thermal cycling is hell on electronics - cracking solder joints and solid state components. You can't just take an ECU out of your Honda, change the software, and expect it to survive on an aircraft - the operational environments are totally different.
Finding electronics that can survive that is expensive, and maintaining them is even worse. If the ECU goes bad in your car, most likely they throw it away and install a new one. But if the ECU costs $50k, you want to be able to fix it. Encasing all the components in some matrix to protect them from vibration (something that is commonly done on automotive electronics) makes them nearly impossible to repair.
Oh, and not many automotive electronics are protected against HIRF and Lightning. Aircraft have to be.