Most animals aren't bothered by flash - they don't change direction, stop what they're doing or really alter their behaviour due to it. It's thought that this is because, to an animal, being hit by a camera flash is a lot like seeing lightning - something they're used to.
Continuous light, such as from a torch or video light, is far more disturbing, since it's clearly unnatural. You won't be using a continuous light in situations where you're just using fill flash, and, in situations where you're relying on flash as your main light, such as night-time jungle walks to spot small nocturnal animals, you're already shining a torch at them to see them in the first place anyway - the flash does little extra to bother most animals, over and beyond what the torch is already doing.