It does make for a nice effect in a video game (and certainly adds some excitement when you're rushing to finish a kill and get back to a station). But...you're right. This seems to be the same in almost all TV and film science fiction.
Star Trek - Let's stick the bridge on the top of the saucer where it's the most vulnerable. Strange considering that they use a large view screen anyway, so the bridge could be anywhere.
Star Wars - The 19km long Super Star Destroyer Executor was taken out by an A-wing crashing into the bridge that stuck up above the main hull of the ship.
Battlestar Galactica - Once again, let's put the bridge at the front of the ship, just above the main hull. Oh, and let's have some large, vulnerable launch bays. What could possibly go wrong?
Hopefully in the far distant future, someone will realise that burying the bridge of a starship deep inside the hull would be safer. Perhaps have some sort of periscope-type arrangement for if the power goes off.