Like everything, there are exceptions. Still, it had to improve your daughter's odds. She just fell in the wrong spot of the statistical curve. Also, consider the possibility that had she been raised on a dairy based formula her problems may have been considerably worse? Could be that she was predisposed to ear problems already. Shape of the ear, genetics, just poor luck.
There is hard evidence supporting this particular benefit of nursing. So personally, I subscribe to the notion that she was still better off in that regard thanks to nursing.
I fully agree about the benefits of breastfeeding. And yes, hubby has had many ear infections as a child, the genetics you mention are probably a very real factor.