Most Americans grew up believing Santa Claus is real. They believed a senior citizen clad in a red suit travels across the world in a flying sleigh every Christmas secretly giving presents to all the children of the world before returning to his elven-operated workshop at the North Pole. They believed this obvious fantasy because their parents told them it was true and in some cases provided falsified evidence to prove it. When children are old enough they either independently discover the fantasy, which is affirmed as such, or are directly told by their parents. No one I have ever met reviles their parents for instilling such a falsehood during the impressionable years of their childhood, because neither the belief or eventual disbelief in Santa Claus is deemed to be harmful.
Indoctrination is the process of instilling concepts, beliefs, or attitudes. In this sense indoctrination is somewhat similar to education. What differentiates indoctrination is that there is no expectation the indoctrinated party will critically question or analyze what they are being told. Children believe in Santa Claus due to the process of (arguably harmless) indoctrination. They are presented a belief and based on authority, in this case the authority of the parents, they accept it generally without question. Confidence in the acceptance of this reality is not based on hard evidence or tangible proof, it is based on the allure of magic and youthful imagination.
Religion is the primary vehicle of indoctrination. Children born into a particular religious tradition are taught to believe it as reality either at home, school, or a place of worship by the authority figures they trust. What makes this process indoctrination, rather than education, is that the child is not expected, prompted, or encouraged to actively and seriously question what they are being told. Major religions have never been comfortable with the legitimate questioning of their most fundamental tenets from outside and youth growing up inside are taught that questions, if any, are acceptable only when basic doctrines remain solidly maintained.
Religious indoctrination is not harmful simply because it teaches children beliefs that are untrue (although this can be extremely harmful), it is harmful because it teaches children to think incompetently. Children do not need religious indoctrination, they need religious education. They need to be taught to think critically, to question authority, to take nothing at face value, and to use information as an evaluative tool. Education would teach children to critically evaluate religion, to honestly and actively question its doctrines, and to utilize information to make reasonable and knowledgeable decisions about religion.