A car might not be an OS, but a modern vehicle is so heavily computerized now that there's a lot you can't do to it without also changing the computer's programming. (By the way, changing a user configurable setting in the interface is one thing, but actually hacking and reprogramming windows or any other program would violate the user agreements and is also one of the things the Digital Millennium Copyright Act is there to prevent.)
In the comments submitted about the Digital Millennium Copyright Act (same link was in the article), the big thing to notice is that they are mainly referring to the computers and programming used on the vehicles. Basically, they want to make it illegal for anyone to mess with the coding and reprogram the settings or create / use third party diagnostic tools to read fault codes off them that would enable repairs (among a few other things). Of course, this approach affects what we can do with the hardware (parts) since modern vehicles are so heavily computerized.
The biggest thing that could affect Jeep owners that I can think of: if I upgrade the tires on my Jeep and regear it to match, what they're proposing would make it illegal for me to use a Flashcal or Procal (etc) to calibrate the settings for the speedometer and odometer. So in that sense, they're forcing me to keep stock tires on it. To me, that's not on and completely contrary to what owning a Jeep is about.
Another one mentioned in the article (less applicable to the Jeep crowd but still relevant as some of us do this), is to prevent someone from changing the tuning settings for the engine performance and transmission.
Of course the big one that affects DIY repairs and independent shops is preventing anyone from making 3rd party diagnostic tools. The article even mentions Ford has already tried to sue Autel US over this under the argument that they must have stolen trade secrets. This isn't so much preventing anyone from using anyone else's parts, but when they make it impossible for anyone else to figure out what's wrong with a vehicle they don't leave many other options than bringing it into the dealer. Honestly, since this would practically shut down independent auto garages I can't see it getting much support. There's just too many jobs at stake. But it's a scary prospect. And the other thing is, when a mechanic is quoting me that a ton of work needs to be done that I didn't bring it in for, I'd like to be able to take it somewhere else for another opinion. If I can only take it to a dealer or approved shop, what are my chances of being able to get an honest opinion about what needs to be done...?