Thanks Kelly and Daniel. ls -l showed that /usr/bin/matlab pointed to the deleted 2009a version.
Daniel's advice worked. Here are the exact commands I used, in case someone else has this problem:
$ sudo rm /usr/bin/matlab
$ sudo ln -s /Applications/MATLAB_R2011a.app/bin/matlab /usr/bin/matlab
Of course, you'll likely have to modify the path(s) above.