Uninstalling NTFS-3G and MacFUSE after upgrading from Yosemite to El Capitan
In order to remove MacFUSE, you can following this guide. So:


Access the root account: sudo su
Execute uninstallation scripts:

/Library/Filesystems/osxfusefs.fs/Support/uninstall-macfuse-core.sh
/Library/Filesystems/osxfusefs.fs/Support/uninstall-osxfuse-core.sh
/System/Library/Filesystems/ntfs-3g.fs/Support/uninstall-package.sh

Additionally you can remove files and directories, that uninstallation scripts don't remove:

rm -r /Library/PreferencePanes/MacFUSE.prefPane


(to remove the button from the preferences)

rm /Library/Preferences/com.google.macfuse.plist
rm /Library/Logs/ntfs-3g_util.log
rm /Library/Preferences/org.catacombae.macntfs-3g.DriverSettings.plist
rm /Library/Preferences/org.catacombae.macntfs-3g.DriverSettings.plist.lockfile
rm /private/var/run/ntfs-3g_daemon.pid
rm -r /private/var/root/Library/Caches/autoinstall-macfuse-core
rm -r /Users/admin/Library/Caches/com.github.osxfuse.OSXFUSEPrefPane