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It is typically true that noncustodial parents have little, if any, say, over the religious instruction or rituals imposed by the custodial parent. But all of this varies state by state and case by case. We know religious division causes great worry and hardship for many noncustodial parents, or parents who share custody, particularly when the religious belief is unorthodox. If you suspect or have been told by your child that outright abuse is involved in a matter related to religion, religious counseling or church-going, most states require, of course, that you report it immediately to child services. If the matter relates to a custodial parent being unwilling, for religious reasons, to take a child to the doctor or dentist for treatment or medical evaluation, especially if the child is ill, this too should be reported immediately to social services for intervention.
Most freethinkers feel deeply that children should not be indoctrinated, and ought to be allowed to make up their own minds about religion when they reach maturity. Even if you cannot stop indoctrination of your child, your example as a nonreligious individual—as someone who uses reason in forming your opinion about religion—ultimately will have a strong impact on your children as they grow up. And it may be highly comforting to a child to know that you don't believe in a hell, or believe that homosexuality is a "sin," etc. A little "cognitive dissonance" can be a great thing when it comes to religion.