I needed to make a change to a hidden file so I pressed Ctrl+H while Nautilus was open in order to see it. For some reason Nautilus took this as "You want to change your preferences to show hidden files also" since Nautilus would show those hidden files by default every time I opened it afterwards.
And it's not enough to press Ctrl+H to re-hide them again, or even to open the View menu and unselect the "Show Hidden Files" option. Nautilus will just open the next time showing all those hidden files again.
The only way to get this resolved for now is to go to Edit -> Preferences and uncheck the "Show hidden and backup files" option.
Of course I am expecting this to be a temporary fix until the next time I need to see hidden files in Nautilus and I press Ctrl+H again. According to this post on the Ubuntu Forums Nautilus has been acting like this for at least three years now.
Any idea when this bug can get fixed?