Open the file /etc/modprobe.d/blacklist as root in a text editor:
vim /etc/modprobe.d/blacklist
Add this line to the end of the file:
blacklist pcspkr
The next time Ubuntu boots up pcspkr will be blocked from loading and you will no longer hear the beep. Peace and quiet at last!
But if you only need a temporary solution to disable the beep, just run this command (as root):
modprobe -r pcspkr