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The concerns are likely just the observed disconnect between their perception of reality and that of others (though more precisely their perception of others' perception). It can be a rough realization, and given that this disconnect is pervasive in the US regarding Israel/Palestine, it stand to reason to be a little bit concerned of how, even Jon Stewart, might seem to perceive that reality.

I'm also only writing this in an attempt at clarifying what the underlying concern might be. With good intentions. I have not seen the clip, so it's not related to anything specific there. Also, I hope it explains why this doesn't have anything to do with being offended or having an inflexible mindset.

Some minds are simply critical of everything. Even their own thought processes, and impose the same requirements as they would on others. This leads to a much higher certainty in that they perceive correctly. If it wasn't, challenging it would be welcomed. Views tend to be highly correlated with the views of others who are similarly critical. It might look like a bubble reaffirming each other's ignorance, because those very much exist. This mindset is antithetical to that. There is no desire to reaffirm anything, only present arguments to re-evaluate. Yet, it often happens that someone you thought had the same critical mindset, reveal small, but exceedingly deep, holes in that understanding. It comes of as hypocritical to that mentality. This is the rough realization I'm referring to. It doesn't offend. It isn't because of a inflexible mindset. It simply disappoints.

Hope that helps. Hope it doesn't offend ;)

Ps: this mindset is also self aware of how arrogant it seems. Ignorance truly is bliss.