Amongst others, one of the husband's right in Islam is to be obeyed by his wife. If a husband is therefore non muslim, he may insist his children are brought up as non-muslims. He may also insist you enjoin partners in Allah (naudhu billah) if his own belief depends on it. To cut it short as I'm in a rush, this is the tip of the iceberg and if this were allowed you can imagine the harm it would bring to the muslim society. But, there is more wisdom then we can see and is it wiser if we avoid questioning the wisdom of Allah subhana wa ta'ala so that we may do not incur sin but increase ourselves in piety.
As I said in my first post, what if the husband allows the wife to practice her religion as she pleases and also allow the children to be muslim. I pointed out another scenario where a woman might not be able to have kids or just might not want any kids, so how does this affect her. Also in Islam kids are taught that their mother should come first before anyone and the father comes second to the mother so the kids will be more obedient to the mom and her teachings. Also in the case where a man might work all day, the wife is with the kids, so therefore it causes her to have a greater influence on the children. Also in case of divorce, children are given in the care of the mom in Islam so, in that case the mom can teach the children what ever religion she wants. So if the husband is muslim but mom is not then she can start teaching the kids her religion and the father can't do anything about that.