It's because him having a "pro vax" person on is incidental, whereas the "anti vax" person is invited because they're anti vax. And you shouldn't be platforming people who spew nothing but falsehoods.
But if you need another example, I'd love to see a single person who stops Rogans randomly inserted anti-trans rants he manages to somehow have on every episode, even if it is not topical. Aside from the fact he had a lot of "anti trans" people on (Debora Soh, Abigail Shrier, Jordan Peterson, Blair White... I mean the list is essentially endless) and not one person who is invited because they're pro trans.
At this point I'm really curious who makes most of the booking decisions for the show. They seem to maximize for right-leaning outrage culture / reactionaries, comedians and some people with very milquetoast politics. I can only remember Bernie as a big left voice on the JRE.