Thinking in terms of a rabbit, these are some sensory information being gathered and thoughts that may occur while being picked up:
1) I am off the ground/my feet are not on solid ground
2) I am not in control of where I am going (I am moving but I’m not moving my legs)
3) I only have half a visual field, hence not fully aware of my surroundings (One eye is blocked by your chest and partially by your arms)
4) I have no way of escaping safely when something dangerous comes (remember rabbits are prey animals; always partially on guard to be attacked)
*Additionally, remember he has no idea of your intentions. He has no idea whether you’re getting ready to drop him free-fall or put him down somewhere for his safety. He’s going to default to the most dangerous at this stage.
When survival instincts kick in, rabbits will think in the moment. It doesn’t matter that he loves you, you always set him down gently, he never bites you, etc.. At that moment, one or all those factors kick his stress into high gear and he’s solely thinking about getting out and back in control of his safety measures. Once the threat (being picked up and put down) is over, then he returns back to normal.
You can help habituate a rabbit to being picked up, but some rabbits will only be able to assimilate so much. Making it seem more familiar, in small steps, is fine, but if you hit a plateau, it may be the limit for him/
The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.