My response will be somewhat different from the others as I am in the EXACT same situation so I will share what I think given my circumstances. I have a daughter born in August 07 and both my husband and I work full time outside the home (he works more than full time as he works two jobs). My mother stays with us from out of state two weeks/month to take care of our little girl and a nanny watches her the other two weeks.
ANyway, for a very long time (the same time frame you are taking about, over a year, basically since she could being to articulate herself), she has a strong and clear preference for me, then grandma, then daddy. My husband fought this at first - he would come home from work and try to hug her and pick her up which she HATED. First, she doesn't really like hugs or being picked up to begin with, and second I think it's because he would get right in her space and while we all now he's her daddy, we all had to be honest in admitting he actually didn't spend THAT much time at home so it wasn't unreasonable for her to be reluctant to have this sporadic close contact.
SO, he's done a couple of things including what one of the other posts said:
1) try to be more engaging around a specific interest or activity rather than insisting on physical affection. Then she warms up to him and before you know it she'll crawl on his lap to read a story or see what he's talking about etc.
2) Also, Grandma, Nanny and I always "talk up" daddy - "Oh, Daddy can't wait to see you when he gets home, he loves you so much and can't wait to play with you or read stories with you or eat dinner with you" - you get the idea. We use our excited vices and talk about how much we love spending time with Daddy and how happy it makes Daddy when we are nice to him because he works hard and he loves us so much. i think this starts to get her thinking more positively about Daddy.
3) we incorporated Daddy into the nighttime routine in a steady way. Since she has a strong preference for me, I always did most of it, but in the last couple of months we started making sure Daddy gets to be a part. Daddy helps get her undresses for the bath, and sometimes gives her the bath. I get her out (she screams if Daddy gets her out instead unless I am not home) and get her into her PJs, then she has to go out into the living room after she gets her bottle (yes she still takes a bottle before bed) and give Daddy a hug or kiss (she always says, I am not giving Daddy a hug tonight but then she'll give him a kiss). He makes a game of it and chases her around "gimme a hug" and she laughs and runs to me, in her room, where daddy comes in to give one more good night kiss. Then, after we read stories and she's going into her crib, I tell her good night and tell her I am sending Daddy in. SOmetimes she says she doesn't want him to come in but he does and sometimes she screams when he comes in but they talk a little bit and then he tells her good night and leaves. It actually is working well and I think helping her be 'nicer" to daddy.
4) we try to "model" the behavior we want. Kids learn by imitating right? So when Daddy comes home, I give him a big hug and kiss and greet him - "it's nice to see you honey - how was your day?" if I happen to be home first (unlikely). My point is we try to demonstrate how we'd like to be greeted - a hug and a kiss - otherwise why would she think it's normal to greet Daddy that way?
ANyway, we are in about the same boat, so I hope any of those might help. Most important is making sure your husband knows it's not personal and it shouldn't be taken that way - he always has to respond by being kind, soothing, gentle and reassuring - if he gets angry he will just reinforce his son not liking him. Everything should be calm and reassuring about how much both Mom & Dad love him.
I cannot see any value in a time out or punishment for your child expressing his feelings. I think that would send a very negative message. Again, your husband is much less close to him than you are due to time spent, it's the reality and it's unrealistic to expect a small child to simply ignore that. Some do but some don't.
Please post again and let everyone know how it goes! Good luck. Feel free to email me separately if you want to talk more.