In my area of CS (artificial intelligence) it seems considerably less popular. I don't really remember how to use it, since the last time I used it seriously was in some engineering (but not CS) courses in undergrad.
You may be right regarding Professors, but that is also changing as they age out.
In the world of electrical engineering Matlab can do things that other packages can't.
From personal experience, I have spent many hours looking at the results of a atan2 function in C++ and Matlab and trying to get them to agree. After a day of work I was able to get them to agree by precisely controlling the rounding modes and using my own atan2 function. This was not fun, and I would rather give somebody 1k to take care of it for me.
Wait, are you saying academia is anti-opensource because of nVidia funding?
I don't see a serious problem with the scenario you describe, though. You're not really describing a hostile scenario, just an affinity for commercial software.
There is a bit of a problem of course; I find a lot of papers that describe how to do things with commercial technology that isn't in the budget. That hasn't been insurmountable for me in any way, but maybe others have had more serious problems with it.
[1]: http://sagemath.org/
NVidia seems to be the preferred hardware for institutions/big companies. I'm not sure if this is because NVidia's architecture is better for supercomputers or if they're simply better at marketing to those types of customers
NVidia funds a lot of academics in my space, and I've found academia to be very anti-open source for those reasons, which amuses me greatly.
Case in point, Matlab. Why is this taught in a world with Python/Numpy/MatplotLib?