Well an operating system talks to hardware and allocates resources, right? The motivation to write a non-toy operating system must be some strong ideas about how to do those things, and they'd have to be pretty fundamental to give up on the vast advantages of interoperability and pre-existing software that would come from just implementing your ideas on top of Linux or whatever.
Past motivations for writing OSes might be expressed as licensing (GNU/Linux), disagreements about fundamental architecture of operating systems (microkernels), need for hard real-time (vxWorks), or the belief that you have the sheer resources and market power to start again and build something better (Windows NT). Security seems like another likely motivation (There's probably a better example than OpenBSD because I don't think they started from scratch).
I quite like the idea that hardware intended for autonomy might benefit from being implemented on bare metal. Devices that AREN'T general-purpose computers, but communicate only with their own hardware and with the outside world by their actions and by communications protocols, well why shouldn't they run on a custom and highly stripped-down OS? You'd expect to get benefits in performance and a smaller codebase for potential security holes. But I don't think the industry is actually headed in that direction.