Yeah, honest journalism and capitalism are hard to combine. In capitalism, companies provide a service that their customers want to pay for. So a paid newspaper publishes news that their readers want to read. Ad-driven news writers what their advertisers want to be associated with. There's little room for reports that are controversial with the readers or advertisers, yet those reports might well be the most important ones.
Well, if they're true. But nobody pays for the truth anymore.
News readers can demand the truth either way (ad-funded, government-funded, corporation-funded, or reader-funded), and they're probably most likely to get it when they pay for it directly. It's the least worst way to get your news I'd say.
This needs to be repeated more often, Chomsky's point is that ad-serving businesses are turning the reader into the product, hardly controversial today considering Google and Facebook are doing the same.
Good journalists and papers are honest about their ideologies, and most editors have written scathing pieces about Trump by now, and the papers reflect these views. It's the ones who aren't honest about their biases you need to worry about.