Mr. Stewart made the remark in 2004 and it is possible that his views may have changed since then. Also, does Jon Stewart know that the comment is offensive? I don't know what his views are regarding our community. The only thing I know is that the majority of the public, including those who accept us, don't understand much about us or know what is and isn't acceptable to say to us and about us.
I found this clip on Youtube from June 3rd where he talks about Caitlyn Jenner on the cover Vanity Fair. Jon comes across as supportive in the clip, although he does illustrate how society and the media place too much focus on looks for women and sadly, Caitlyn is no exception.