Flash Fire is probably my favorite rune, and by far one of the highest DPS primary attacks you can put on your Witch Doctor.
Although it seems like you're going to be doing less damage by using it, in fact I've found that I do far more with it. The limited radius of the standard skull explosion is dwarfed by the range on each individual bounce with Flash Fire. The casting speed and homing ability also mean that you're doing consistent damage to multiple enemies regardless of how they shift around the screen.
The skull also bounces and homes in even if it hits nothing on the first bounce, so long as there is a target in range of the second bounce. You can, for instance, let your pets or follower tank a respectable distance away from you, and just arc the skull in their general direction to pile on the DPS. The homing also makes it a "fire and forget" attack, so you can be paying attention to other, more important things, like getting out of the way of desecration/molten patches, or checking your skill cooldowns. It's essentially an attack that never misses!
As a lesser benefit, the skull will also target breakable objects, so getting "Destruction" bonuses is trivial with this rune.
When you're in the situation where there are more than 6 enemies in close proximity, or their health is very high, your FireBomb attack is not your best bet. Switch to a mana draining area of effect attack like Zombie Charger or Fire Bats, and you can do far more DPS in far less time.