There are just enough similarities, or commonalities, that I can see why some comparisons are made. I have no problem with Harry Potter and Name of the Wind being compared as long as the comparison isn't the last word on either of the two works.

Magic Academy
Struggles verses the different classes at the Academy
Bitter personal rivals and rivalries
Good deal of time spent bending rules and sneaking around
Some faculty supporters and some faculty detractors
throw in some fantasy tropes/themes

There is certainly enough there to draw some comparisons and contrasts. Neither should be reviewed or rated on a scale of how they hold up to each other. I can be interesting in looking at how the two compare on contrast in those areas where they are dealing with similar things.

For the most part, from what I've seen in some reviews, there is a segment of the reading population that goes overboard in negatively criticizing Name of the Wind using Harry Potter as a measure. That is fairly ridiculous.