I'm having this problem, about 3 years later than the original post. I'm running OS X Yosemite 10.10.2 and recently the menu bar and dock have disappeared from Safari (only Safari - when in Word for example its all there). If I hover over the menu bar it shows up but its still annoying not to see time, battery charge etc. I can't see the dock at all. I've tried all the things mentioned in this and other sites but to no avail. I can't see any 2 arrow box thingy on the menu bar to unzoom, I've quit Safari and re-opened multiple times, if I use escape it just reduces the size of the whole screen, if I go view and zoom in and out it just reduces the size of the whole screen, I can't simply resize the screen because now I don't seem to be able to get to the edges of the screen and can't see the resize option. Only thing I can think of that may have caused it to start is that I used Command/ scroll to increase font size.
Is anyone else having this problem and can anyone talk me through things to try?