What has changed? How do I fix it?
That is pretty little information to trouble shoot. Can you give more information like when the problem started, which version of Ubuntu you are running, and which version of Mate you are running.
Is the root folder there (with an x or lock)?
Are you opening Caja as sudo(root yourself)?
Are you clicking "show hidden files"?
If all the answers are yes, root files should be showing.
If you are doing all those and root is still not showing, then give/ leave some more information. like when it started, say after an update or after a certain installation or after you made some modification.