Some of the arguments aren't actually Olympian, although if you have a pre-existing bias against commerce or capitalism it may feel that way.
Most obvious example query of where PageRank totally fails: [flowers]. The correct top result here for 99.9% of searchers is a local flower shop or possibly a big flower delivery chain, but it's not the Wikipedia page for flowers. Likewise for [hotel near me] which an algorithm like PageRank will yield garbage for, [oppenheimer showtimes] and many other very popular query types.
Link based ranking just doesn't work for this sort of result. You need data that isn't on the web which means you then need a way to rank it. And how exactly do you plan to rank flower shops or movie theatres? You've got no data on which to do that. Even if they have a website at all (big if) people don't organically link to them. Attempts to gain ranking data via things like user reviews will fail, almost nobody real reviews local stores or cinemas so if you rely on that then either you'll be flooded with fake reviews, or companies will aggressively push people to write them, or both, and users hate both outcomes.
Ad auctions work much better. Users don't have to do anything directly, they just buy things from the best businesses as they see it, revenue flows to those businesses enabling them to bid higher for ads, so users see the most successful businesses as determined by the market as a whole, which is much harder to game than user reviews or PageRank.
When the original Google was built, it was built by students. Their first ever test query was the name of the guy who ran the university. Their edge was ranking publicly available web pages using link graphs, so they just weren't thinking about commercial queries at all and if that's the scope of your ambition then yeah it will look like ads are always a conflict of interest because the only model you can imagine is re-ranking organic informational results surreptitiously. Once they turned on their first search backend deal and got experience running a search engine with serious non-nerd user traffic for the first time, they realized there were tons of popular queries that their whole approach just sucked at and would always suck at. That's when they realized that in some cases "ads are information", as they put it.
That wasn't some sort of paycheque-induced intellectual blindness, if it was then Google would have gone bankrupt a long time ago. It was an actual fundamental realization about the nature of what people use search engines for.