It is intended behavior. If you want to run your application automatically on startup you should modify /etc/rc.local file which is the startup for your raspberry pi. I would recommend adding the following lines at the end of the rc.local file.
Try the Manage Add-Ons workflow. Go to MATLAB toolstrip and click on Add-Ons and select Manage Add-Ons. Here uninstall the Simulink support package for Raspberry Pi first and then uninstall the MATLAB Support package.
Best Answer