It doesn't have to be necessarily root, even a limited account could be enough for many things (and some traditionally root-only features like ability to bind to lower ports can be handled using Linux capabilities without compromising whole system). You can use the same argument against that too. And of course there are other systems that are much more open. But (to take a shortcut) none of them has WinBox.
I always liked Linux, but at the same time, something was missing. First time I got to RouterOS, I immediately knew what it was.
Truth is, I'm not even completely sure if I want the ability to run own stuff. What I really want from MikroTik is just few small additions/fixes here and there and I'd be happy as a clam. But as we all know, waiting for MikroTik to implement some features could take forever. So the ability to have some level of DYI possibilities could perhaps be the best solution after all.