Religions indoctrinate through churches and governments and broadcasts and books, but mainly through parents.

Parents are the worst.

To indoctrinate a child is one of the most vile forms of child abuse.  It limits that child from having as full a life as might be.
 
Religions, of course, aren't the only things that work to indoctrinate us.  I would add businesses, both as sales organizations to sell something and as employers, and of course political parties and the adherents of no end of quasi-religions ideas and ideological movements.
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Propaganda is I think the main tool of indoctrination. Stir up the person's emotions -- people love children and puppies, so put pictures of little children on your soup can or a puppy on the cover of your book. People hate, so put pictures of atrocities, both real and invented, in your film. People are patriotic, so wear a flag pin and have flags in the background and patriotic music accompanying your commercial. People want to be accepted, so imply that those who think otherwise are outsiders.
 
Finally, we all want to live forever, so teach a wonderful afterlife. This also can be used for people's desire for revenge.
 
Logic and reasoning can also be propaganda when it is in the form of false evidence or pious fraud or cherry picking the evidence.