One of the classic books on the subject, Modern Operating Systems by Andrew Tanenbaum, used to focus on Tanenbaum's own pedagogical Unix OS, called MINIX. More recent editions focus on Linux (which Tanenbaum would say is based on Minix, whereas Linus Torvalds would say otherwise), though at least a third of the book describes Windows as well.
Even if Windows were open source, I think it's likely that due to Tanenbaum's influence, Linux would still be the go-to OS for OS classes.
It also conveniently offers a comparative perspective for most people, as Windows is the OS that most people have been brought up on.