I am the non-birth mother to our two children - one is almost 5, the other is almost 5 months. From the start, the older child has preferred me. I think there may be a few reasons for this - he went to the NICU after he was born and because my wife had just given birth and was less mobile (and absolutely exhausted), I was with him a lot during his first few days. He easily took a pacifier so after she finished nursing him (for about the first year of his life), she'd hand him over to me and we'd go nap or hang out to let her rest. I am a teacher and so we had more time together in the afternoons/evenings because DW got home from work later. I usually dropped him at daycare in the morning so we spent more time together on that end as well.
With the 5 month old, I can already tell that he prefers her. Part of it is that he's a little fatty and loves to nurse. I think another big part of it is that he wasn't taken away after being born and didn't require a NICU stay, so he nursed immediately and bonded with DW immediately. I cannot take him away from her to let her rest and console him as I could with the older child.
As the older child has gotten older, he and DW definitely have their own special bond that has grown since she now works from home. I imagine that her bond with the younger child will continue to grow since he has been and will remain at home with her until he starts preschool at age 2/3.
I agree that you should try not to take it personally, and maybe try to carve out more "special time" for the two of you. Do you each spend equal amounts of time with the child? Do you both work? Perhaps that is a factor in all of this?