I agree with you that children need to think for themselves! Our survival as a species depends on freedom and fresh ideas.
But I think questioning your ideas about authority and compliance are a good place to start. Now, this normally sends perfectly rational people into a panicked frenzy but just because you consider and ponder something doesn't mean the world is going to come to an end.
It's about working with your child versus being in a top-down relationship. It doesn't mean they'll run rampant over you either.
Check out Leo Babauta's post:
On Compassion Towards Our Children | Zen Habits
Also, anything that Alfie Kohn has written is wonderful - he writes a lot about how children are motivated. His book, Unconditional Parenting, is awesome. Website: alfiekohn.org
You might think back to your own childhood, too, and consider how you ended up thinking for yourself!
So glad that you brought this up! Your child is very lucky to have a parent like you.