You can uninstall or removes an installed bedtools package itself from Ubuntu 16.04 LTS (Xenial Xerus) through the terminal,
$ sudo apt-get remove bedtools
If you would like to remove bedtools and it's dependent packages which are no longer needed from Ubuntu,
$ sudo apt-get remove --auto-remove bedtools
If you use with purge options to bedtools package all the configuration and dependent packages will be removed.
$ sudo apt-get purge bedtools
If you use purge options along with auto remove, will be removed everything regarding the package, It's really useful when you want to reinstall again.
$ sudo apt-get purge --auto-remove bedtools