Making it work with Linux and OS X was very trivial for myself but it may not be for others. Since it's just C the Arduino part was easy. The mex files were only compiled for Windows but compiled just fine under Linux and OS X.
The rest of the build process requires a few tweaks but other than that it works just fine. (There is still an error in actually making it, but running 'make -f' from the command line works just fine). There are also some very simple errors such as if 'boards.txt' isn't formatted perfectly that need fixing.
I'm trying to fork it and document all of my changes however I just read through the license and it doesn't look like I can do this. So I may just be releasing .patch files so that everyone on OS X, Linux and Windows can use their Arduino with Simulink. (Unless that is prohibited too, I'm an engineer not a lawyer).
I thank Mathworks for extending help out to the Arduino but it falls just a bit short by prohibiting anyone from fixing the basic problems.