Hi A.,
We are also a military family, so my heart went out to you when I read this because I understand what you are going through. My husband went on a 3 to 6 month deployment every year for the first three years of our daughter's life. It was very difficult for her and so difficult for him that he called me from Iraq and said, "I just did the math and I am going to miss a quarter of her life. That means by the time she is 16 I will have missed four years worth of that time. I don't know if I can do that." Two more kids and 6 years later we are still in, so we had to figure out a way to make things work.
It may not be anger, per se, as much as it is the fact that you are the constant. You are the one she goes to for things the majority of the time, you are the one setting boundaries and carrying out discipline which actually creates a comfortable home for a child. So, she will prefer you.
One of the things that helped us was that we put our children in situations where I was gone and dad was the one there with them. While they, at first, didn't like the separation, they learned to go to him and lean on him because he was the one there with them. It gave them time to bond because their first choice (me) wasn't there to turn to. If this meant that I left through the front door and crept in through the back to head for the bedroom then so be it. I took a lot of long baths. I went to friend's houses for coffee, saved errands for when he was home and went alone. In the end they began to develop that relationship with him. AND it was actually good for me to have time to regenerate and recharge. I needed that time more than I realized. It felt good to give up some of the responsibility and my faith and trust in my husband grew even more when I saw how capable he was. I had no idea I could love and admire him more, but it turns out I was wrong.
Another thing would be to have him step up with the discipline. As crazy as it may sound, for your daughter to see the two of you as equally, you have to take an equal part in the parenting. I know it is probably the last thing he wants, to be gone for three days and then have to come home and be "time out guy", and it probably really is when she already prefers you. But it will change how she views him and his role in her life.
Hope this helps, and God bless you for the sacrifice. Your husband serves his country, but so do you and your family.
L.