A missing or kidnapped child is just that, regardless of who the individual is who takes them. If it is a biological parent who takes that child illegally then an Amber alert should be issued. The alert is to help find the missing child and return them to their home.
If a parent does not have custody or strict custody rules (such as supervised visitation), then there is usually a pretty good reason for this. Just because a child is with a biological parent doesn't mean he or she is safe. Sometimes a parent who illegally takes the child is honestly trying to get their child out of a bad situation, and that is very unfortunate in those instances. But since most of the parent kidnapping situations are not justified, the law has to stand.
If a parent violates a court order and takes a child and there is a concern the child could be in danger, then an Amber Alert should absolutely be issued. There was a case here in California this week where a mother absconded with her seven month old and kept the child in a bag. This is highly unsafe and erratic behavior.
Yes, Amber alerts should be issued for parents who take their kids because many of them do not have legal custody over their children. Therefore, they are taking their kids from someone who actually has legal guardianship. This is unfair to the true guardians and the kids deserve to be home with those who will protect them.