An obvious reason is that the manufacturers do not want to deal with warranty issues. Of course you can probably understand that the possibility is there that bad software can result in engine damage. This applies to other systems, too, for instance the guy who demonstrated that he could alternately flash his headlamps like a police car by sending traffic to the lamp controller probably does not realize that he should not be reigniting the HID lamp every couple of seconds, because this will shorten its life.
The automakers are liable to laws in every developed country. The United States has these average fuel economy laws that the carmakers must meet, and in some states, harsh emissions regulations must be adhered to and guaranteed. The emissions testing regime in some of these states has done away with exhaust gas analysis and relies on the engine control's self-diagnosis to show that the vehicle is performing to spec.
However in other countries, increasing pollution emitted by a car constitutes tax fraud.
Road safety is also important. One German carmaker uses the same diesel engine for a range of vehicles which have differing performance levels. I thought it was clever when I found that you could change the low market six cylinder from a cheap model to give the power output of the top model of the range simply by carefully changing eeprom data. But the low market model has a lame exhaust and small brakes. Triple the engine output power and this is potentially a disaster.
For as long as the universe of tinkerers will include those without experience or scruples, the carmakers will have to keep developing anti-tampering measures to show that they are attempting to guarantee that their products will perform within the bounds of the law, and indemnify them against bogus liability and warranty claims. Some tinkerers are smart enough to see the big picture and think about the results of what they are doing. Others either don't realize that these systems were designed by teams of engineers with more degrees and experience than them, or figure that they can sell genitalia enhancements to any twentysomething that walks in the door. These are the guys that scare me.