Bernard Goldberg is an isolationist conservative. Jon is a social progressive. This was an oil and water interview.
Moderate conservatives who hold strong opposing views don't frequent the show, and only when there is a book to sell, so Jon probably took the opportunity to grill the only one that will cross his path... for the next 13 months.
Colin Powell on the other hand, is a prime-rate dissembler, and someone who can pretend to believe in something, plus he has incredible political power -- you just don't really know what a man like him truly believes in or what he can do to you, and Jon was really flustered, maybe even scared by him. He made that one a "fun and funny interview". Goldberg was easy pickings though.
Bernard Goldberg "lost" the interview. He let Stewart speak his mind longer, he allowed interruptions, and he failed to play devil's advocate, which is how Jon rebuked him on each point. That "Bigot Channel" thing was a "look, I'm so right because I'm exagerating my point and showing you how culture really is evil!" and earned negative credit.
Oh, and on the Amazon page for this book... the reviews... it's like a comments section at a blog where liberals and conservatives can post at the same time.