Flat feet have a direct relationship in how a bunion forms on the foot.  There is a very complicated process that begins from when a child first starts to walk that ultimately leads to the development of a bunion, and this bunion continues to develop over a lifetime of walking after it initially forms.
 
The steps that lead to a bunion can be summarized in the following paragraph.  Keep in mind that this gradually occurs over time.  There are a smaller number of children who are simply born with an abnormal bone position that is technically a bunion.  However, most people gradually develop their bunions well into adulthood.
 
The foot, as it flattens out, becomes unstable in the middle of the foot.  As the middle of the foot loosens, the area along the side of the foot where the big toe sits becomes more mobile, and pushes upward and rotates inward.  As the big toe joint looses the ability to flex upward enough during this motion, the big toe begins to drift towards the second toe, and rotates outward.  The long metatarsal bone at the base of the toe is soon pushed towards the side of the foot, becoming prominent in the process.  Once this rotation occurs, all the various soft tissue around the joint and the tendons that attach to the joint begin to adapt, and actually contribute to worsening the bunion over time.  The bone and joint surface even adapts to this position, leading to joint compression, and eventual arthritic change.  In advanced bunions, the arthritis can get so bad that the joint can't move well at all.
 
The use of orthotics to keep the arch structure stable is very helpful in delaying the above process, and limiting the development of a bunion deformity over time.  While they cannot fully prevent bunions from forming, and cannot reduce a bunion deformity that has already developed, orthotics can be an important part of the treatment of a child with flat feet to help prevent significant bunions from forming later in life that may require surgery to correct.