Teaching kids to question also means that you have to facilitate their questioning you. There are effective ways of doing that.
You begin with giving them input and options within parameters that you are comfortable with, and that allow for safety. A big part of this is following through with the consequences of those choices because learning to question, with integrity and not just to cause problems, requires critical thinking. Critical thinking, requires, among other things, that a person is able to consider the bigger picture and see beyond their immediate actions.
So a child ends up having input into perhaps discipline, and the discussion allows them to question (that is to challenge) your ideas. Once the decision is made, that challenge is over with. When to challenge is also key.
People question, but they ask the wrong questions at the wrong time and teaching a child how to do this effectively is key. You are part of the jungle gym on which they will develop their muscles.
We found it helpful to have many discussions with our kids, where their input and ideas were accepted and explored and we often left discussions open ended with perhaps more information needed and to be picked up at a future date. We taught them to question with respect. We taught them to think about the questions they were asking.
You can also think about your own response to when people question you. Does it annoy you? Do you get defensive? Or, do you take it as an opportunity to think about your position, to share that process, or to even possibly to find out the reasoning behind the questioning, which can often provide you with information you might not have had, or provide, at least, a different perspective.
No-one should ever object to being questioned. If something is right, true or above board, it should be able to stand in the face of all questions. The moment that someone suggests that there is something wrong with YOU for asking a question, or that it is disrespectful to the subject matter to not blindly accept it, then you know you have entered the realm of mind control and people who have something to hide. Period.
If that does not impress upon you the importance of teaching your children to question everything, then nothing will.