I would make a symbolic link to the binary instead; type as root :
ln -s /home/your_user_name/usr/local/MATLAB/R2011b/bin/matlab usr/bin/matlab
And i suggest you avoid the ~ shortcut anyway in configuration files.
P.S. Do you really have a /usr/local directory in your /home/your_use_name directory ?
Other than that, please indicate which distribution and desktop you use to help answer your P.S.