It doesn't matter if they teach you C, C++, FORTRAN, COBOL, Assembly, Visual Basic, LISP, Scheme, etc.
It doesn't matter if they force you to use emacs or vi.
It doesn't matter if they use Windows, UNIX, Linux, etc.
It isn't what they make you use. It's what they teach you that matters. A good university will teach you the ideas behind computing - how operating systems work in general. Nor should a university be predominant in any given language - they should be exposing you to several different languages that showcase the fundamental differences between them (i.e. procedural vs. functional vs. object-oriented).
What matters is that whatever it is that they teach you; will allow you to take any of the above technologies and be able to become proficient and productive with them. People get bent out of shape over a particular technology, but particular technologies either evolve or fade away in time. The foundation that was taught to me in university was sufficient to allow me to adopt new technologies, understand them and implement them within any environment as required.