It is actually proven that infant GIRLS tend to reject their fathers, and all other men. Of course a boy can do it too, but its not nearly as common as in baby girls. There are theories as to why, but no real answers.
The positive thing is that they DO grow out of it.
From almost the time of her birth my daughter, now 2, rejected her dad. He was nothing but nice (actually created a problem, he's afraid to discipline her much because he so badly wants her to LIKE him). She wouldnt let him bottle-feed her when I weaned her, wouldnt let him spoon feed her either, no diaper changes, no games, no holding his hand even. She would even freak out if he gave ME a hug by the time she was about 18mos old. Yes, it got much much worse as she older.
But then, slowly but surely, as she got older and less dependent on me, she began to decide that maybe, just MAYBE, he wasnt quite as bad as she thought. Last night she got really mad at me (she wanted to get a brand new banana instead of finishing the one she started 1 hour prior. I of course told her no way, which because she is a typical emotional 2 year old girl got her bursting into massive amounts of angry tears.) and ran off immediately to her father, crawling into his lap and putting her head on his chest, telling him all about what the big bad mommy had done! (He did back me up and say no, she has to eat the first banana, well, first.)
So trust me, if a girl as anti-dad as Claire can come around any kid can.
Remember that is actually natural, though not well understood. Make him stay involved. Remind HIM that babies cling to mommies- his time WILL come too. Promise. :-)