Matthew 7:7 is often quoted to suggest that one should never challenge someone else's beliefs or actions. To that reading, "Judge not, that you not be judged.." would seem to be an absolute prohibition on critical thinking.
Let's try this one together. Read the passage in it's immediate context (below) and see what you think? Also check against the parallel passage in Luke 6:37 and following.
"Judge not, that you be not judged.  For with the judgment you pronounce you will be judged, and with the measure you use it will be measured to you.  Why do you see the speck that is in your brother's eye, but do not notice the log that is in your own eye?  Or how can you say to your brother, 'Let me take the speck out of your eye,' when there is the log in your own eye?  You hypocrite, first take the log out of your own eye, and then you will see clearly to take the speck out of your brother's eye.