DS9 features terrorists and doesn't paint them all as villains. I imagine this likely infuriates Stan Smith which is why he can't stand DS9.
Actually, the irony is is that when he made that comment, it's about surrogate births. "I've never heard of this and I've seen every episode of Star Trek. Wait, is this Deep Space Nine?..." DS9 of course, is the only Trek series to feature a surrogate birth, so whoever wrote the episode clearly doesn't hate DS9 and is very familiar with it.