The episode mentioned in this post is available in its entirety on The Daily Show website. I had to remove the link to it, since this is only my second post. They start the Naomi Watts part around 16 minutes in, it doesn't get relevant till about 18:35 however. I wouldn't read to much into what he said, you have to remember it is a comedy show. I suppose when the actual benefit airs on TV, we will get a better view of Stewart's opinion on Autism. It is currently set to air on October 21st 9pm / 8pm central.
According to Comedy Central, the benefit raised almost 7 million dollars. As for where the funds raised will be spent, the following is copied directly from the comedy central website.
"Night of Too Many Stars" will benefit a variety of autism education and family service programs across the country, in support of the overabundance of autistic individuals that so desperately need quality services. One exciting new initiative is The Institute for Brain Development – an all-inclusive diagnosis and treatment center positioned to undertake groundbreaking collaborative research into the causes and treatment of autism spectrum disorders. The Institute is the product of New York Center for Autism's partnership with New York-Presbyterian and its affiliated medical school of Columbia University College of Physicians & Surgeons and Weill Cornell Medical College.
And finally from the Autism Speaks website: A portion of the proceeds will benefit Autism Speaks. (In reference to the aforementioned benefit)