First of all, there is difference between "Desktops" and "Window managers" in Linux. "Desktop Environment" usually includes a selection of software that is integrated together, such as file manager, text editor, control panel for system preferences and so on. In contrary, Window manager is one (but important) component of a desktop that handles windows, and may be used on its own. You may swap one window manager with another, for example, I use XFCE desktop with OpenBox window manager.
So, Desktops come with selection of software and some default settings that allow that software to interact in a way that was intended by desktop authors.
But first problem is that when you install another Desktop Environment to your machine, old software that was included with default DE is still on your system, so often you will end up with several programs inteded to do the same task (i.e. for text editing - Gedit on Gnome, Leafpad on XFCE and KWrite in KDE). So some users will prefer to have desktops pre-installed.
While the problem of software duplication may be solved by installing minimal system and then installing your DE of choice, there is second problem: there are some tweaks, pre-made settings and patches that make your desktop environment more usable.
People who maintain their "flavor" of distribution (such as Kubuntu, Lubuntu, Xubuntu etc) are usually well-aware of specific issues both to their DE and base system. So usually big distros have their variants for various desktops as do Fedora (they call it "Spins") and Ubuntu. Also they test and provide community support, while company-backed "main" distro may have more priority support for default choice of software.
And while not being different operating systems, different DEs have slightly different paradigms and quirks. Also they have various resource requirements, good and bad points, metaphots, so for regular non-technical user they appear as different OSes.