Read the first page of this: http://www.justice.gov/atr/cases/exhibits/1584.pdf
The BeOS is bundled with the machine and is already pre-installed
on the hard drive. As shipped from the factory, your FLORA Prius
will NOT boot the BeOS...
I don't think BeOS would have got very far even if there was no deals against it. After all, there was no massive support from publishers to develop for it, and an OS without software remains a small, niche market. Windows was already huge at the time.
Now, I agree there are probably better OSes out there (either Linux distributions or others) but it all boils down to "what is the platform people develop for". Mass acceptance requires your OS to be able to run enterprise applications, modern games, and to run flawlessly (or at least without major issues) on a good range of hardware. It is very difficult to pull this off unless you have a great amount of ressources nowadays.