Are Schools Institutions of Marginalization?

In reading "The Art of Nonconformity" by Chris Guillebeau, I came across a quote:

"Unreasonable," unrealistic," and "impractical" are all words used to marginalize a person or idea that fails to conform with conventionally expected standards."

Is it just me, or are our schools essentially tools perfectly designed to marginalize those that lie outside our seemingly arbitrary standards?  Are we doing our kids a disservice by rejecting those students that do not perfectly fit our "ideal student" stereotype?  

We like to claim to teach critical thinking skills, but how often do we support kids that think critically about our schools?  

Here's a hypothetical situation:

Timmy is a kid in your third hour class.  You are presenting a well-planned lesson that has resonated with students in the past.  Timmy does not see the value of the project and demands to know why he has to do it.  You give him your rationale, which is educationally valid based on our training as professional educators.  Timmy rejects our explanation and gives his own interpretation of the lesson.

Do we credit Timmy for thinking critically?  Probably not.  In all likelihood, we punish Timmy because he's being insubordinate.  We marginalize Timmy because he disagrees. 

When we ask kids to think critically, wouldn't it be more accurate to ask them to think critically as long as they do not question our roles?