But then you never explain why you would want autofire on. In order to focus fire on a system and take it down, you want all your weapons to fire at the same time, which means having autofire off
Ah-hah, this is a common misconception! You can have autofire turned on and your weapons will not fire until you give them a target! My recommended technique is to un-target things and let your weapons charge. They won't fire without a target; so it is safe to leave autofire toggled on. With this method you Pause, Target, Unpause - and your weapons will all fire at once the moment you unpause.
I have found that its really easy to get caught up in a battle with autofire turned off and waste many seconds with your weapons not firing. Leaving autofire on means that if you forget to clear the target after each firing, your weapons will still ping away at the enemy. Since you're likely to have some combination of Ion and Missiles (in addition to lasers), this means that you'll at least be harassing the enemy (damaging hull or ionizing shields) even if you aren't maximizing your fire. And once you get their shields down with a few well-timed volleys, having your weapons firing consistently (leaving a target locked-on and leaving autofire on) is the fastest way to destroy the ship - you don't need to fire in volleys (in fact, you often want the weaps cycling as fast as absolutely possible so you can keep their weapons and shields offline - autofire is better at this than you are).
So IMHO its "safer" to leave autofire on, and use your targeting (as well as the pause key) to get your weapons to fire as a volley when you need it. Try the steps exactly as I've written them, and you'll see what I mean.
--Noel