I'm using ubuntu 11.04. I ran the script by marking as executable, double clicking on it and selecting run in terminal.
The script worked fine and I can run minecraft using dash, the icon on the desktop or by typing 'minecraft' in a terminal.
I think this might be a bug in unity rather than the install script as I have experienced the same problem when clicking on other launcher items.
If you edit the minecraft main menu entry so that it is an 'application in terminal' it will always work but you will have to put up with two items in the launcher when you are playing minecraft (because the terminal comes up too).