It's reasonably safe; I've noticed some people saying no one should use rpi-update unless they have a good reason because the kernel is ahead of the standard Raspbian one (and hence, less tested in the field) but I have never had or heard of an actual problem resulting from it.
A potential issue is that Ubuntu updates could then overwrite your newer kernel with an older one, since the practice is to always name these kernel[7].img, regardless of version. I don't use Mate, but I do use ARM distros that aren't intended for the Pi at all and hence install useless things in /boot, creating a similar potential conflict. My solution to that is to mount the first partition on /boot/BOOT instead (this requires editing /etc/fstab); that way the distro can put whatever in /boot, which is now just a regular directory instead of a mount point.
That strategy would make using rpi-update awkward, so I just copy stuff in from a git clone of the firmware repo (which includes everything rpi-update installs: the kernel and modules, firmware and device tree stuff in boot, library stuff in /opt/vc). Alternately, you could instead leave the first partition completely unmounted (the mount serves no purpose except for updating the contents) except for when you want to access it, or run raspi-config -- then you would mount it on /boot, the normal contents of which (the Ubuntu installed stuff) will then be unaccessible, but no harm will befall them. If this is confusing, copy some files into a directory normally used as a mount point, then mount something on it. Notice those files are not there anymore. Unmount and presto -- they are still in the normal directory "underneath" where a device was mounted.
Just remember to unmount after you run the update.
