And if it is a temper tantrum, then maybe you can get him more in the mood by giving him a treat after you do pick him up to associate the two together. But there's a danger that he'll associate angry squeaking with ways to get food.
I have three rats. The oldest is perfectly fine being picked up. She's very sweet. The youngest struggles with being picked up at first and will curl her toes when clinging onto your arm (not sure how to describe it but there seems to be a way a rat grabs you when she's uncertain about her surroundings). The middle one actually scurries away if it looks like you're going to try to pick her up. When she is picked up, she whimpers and also curls her toes when clinging.
The funny thing is that even the nervous rats will come up to me all lovingly and kiss my fingers. The middle one often puts her front paws on my hand while safely keeping her haunches in the cage. When they're riled up (usually in the evening), they're perfectly happy jumping up on me and crawling along my arms and shoulders—as long as I stay near the cage so they can hop off when they want. They're very confident when it's on their terms. When I pick those two up without permission, they don't like it (but the youngest is coming around, just not as relaxed as the oldest yet).