Indoctrination "is often distinguished from education by the fact that the indoctrinated person is expected not to question or critically examine the doctrine they have learned." (Wilson, J., 1964. "Education and indoctrination," (Manchester University Press). In other words, indoctrination is "dogmatic."
We need to distinguish between teaching children "what" to think from "how" to think for themselves, i.e., asking how we know what we know.
“Do not indoctrinate your children. Teach them how to think for themselves, how to evaluate evidence, and how to disagree with you.” (Richard Dawkins, The God Delusion)
Indoctrination is teaching children rote dogma, i.e., beliefs that are to be accepted on authority alone. Education on the other hand does not require uncritical acceptance of doctrine. Moreover, a good education encourages critical thinking and provides students with the cognitive toolkit to acquire knowledge for themselves, i.e. the scientific method. The scientific method is about asking why things work the way they do and how we know it, how we can test our hypotheses against the data -- not simply accepting things unquestioningly. If a child asks me what table salt is made of, I can reply, "Salt (NaCl) is a molecule consisting of one atom of sodium (Na) and one atom of Chlorine (Cl)," but I can also describe what that means and how we know that, how different elements behave, (their properties), and invite the child to test this for herself through experimentation. If a child asks me how old the earth is, I can explain how scientists estimate geological ages of things using radioactive isotopes, dendrochronology, plate tectonics, etc. to arrive at an estimate. The important point here is that scientific knowledge can be tested, at least in principle. A good hypothesis must be predictive, theoretically falsifiable, and open to revision. We need not hold beliefs dogmatically; we can go out and check how the world works, look at the evidence, and go where the evidence takes us. Scientists do not claim 100% percent certainty in their claims. If new data come in that conflict with the current model or theory, we must revise our theory. Indoctrination on the other hand requires only that we unquestioningly accept what we are told. Religious indoctrination is a good example. Religion is not self-revising. Religious "truths" are held dogmatically. Religious parents will often teach their children a collection of unfalsifiable bronze age myths that must, again, must be accepted on faith. But parents can opt to educate their children rather than indoctrinate them by teaching them how to think for themselves and by providing them access to teachers and scientists who can explain current theories and, more importantly, how we have arrived at them and how we can test our assumptions.