Babies have no sense of good or bad behavior, so I hope you won't label her honest and natural response as such.
There is apparently something about the way your DH looks, smells, or holds her that is not comforting to her, and at only 3 months, she is all about comfort and security. If Daddy is tense about not being loved or anything else about his relationship with his little girl, that may very well be transmitted through his body or voice to her, making her further ill at ease.
Try lying in bed together, with her in between the two of you. Daddy can gradually increase the amount of interaction with his baby at whatever pace she'll accept without upset. I'll bet in a couple of weeks or so, all will be well.
Be aware that young children go through natural (but disturbing to parents) phases of preferring one parent over the other. At some point she may want Daddy only, all the time. Those preferences are hard to explain, and can switch from week to week. Don't take it personally – she'll just be (very clumsily) exploring her full range of emotions.