Your son may see them as competition for food, toys and affection. Ensure that he has adequate attention when the animals are around and not abandoned when your pets approach.
You can show the toddler that animals that are mistreated will sometimes fight back. If he/she sees that certain animals can become dangerous if instigated, then it is more likely that he/she will be far less aggressive toward them.
Demonstrate kindness towards the animal, show him how to pat the animal, speak to the animal in kind tones. Create bond between them, address their names in sentences binding them.