when my baby was newborn, she cried every time i held her, except when i was nursing her. any other time, she'd cry. it used to frustrtate me a lot, and i think for the first 3 mths, i didn't hold her at all, except when she was nursing. my husband said i was very tensed & nervous when i held her, and my baby picked up the stress from me. (i was suffering from post-partum depression, so i must have bn very stressed out). eventually when i made a conscious effort to relax before holding my baby, she stopped crying when i held her. so i guess maybe your husband is generally stressed & your baby picks it up. some babies are more sensitive than others in picking up emotions.
pls talk to your husband gently about trying to relax (like watching a funny tv show or obeserving his own breath for a few minutes) before he holds you son. and pls remind him that a 3mth old is fragile in every way, his bones can be easily broken, skin easily bruised, brain easily shaken, so please don't hurt him. stay around when he's holding him, take over once baby starts gettng tensed & cry. let your husband know that eventually he'll be able to hold him. maybe put baby on the floor, on a blanket, both of you sit next to baby & coo with him, so that your husband is feeling that they're bonding too.
good luck!