I've been out of that business for a long time now, but short answer is yes, absolutely. Yes, it might create problems - there is always and has always been tension between editorial and business. This can definitely be a problem at the local level, it's gonna be hard for a small paper to run a negative story about a big industry or company that's the biggest employer in a town or region or that advertises heavily in the paper, eg real estate firm or the like.
I have had stories spiked because they were 'too political' and that sucked. And I've quit jobs for ethical reasons (though not in that same context), which also sucked. I think your criticism is valid but I also think that an overly ideological analysis - which a guy like Noam Chomsky does a lot - can mislead one into oversimplifying a complex picture. Understanding the idea and mechanics of manufacturing consent is important for media literacy and political understanding. But it's a rule of thumb to keep in mind when consuming media, not an iron law of social behavior; if you start assuming that everyone in the media is part of a giant consent-manufacturing conspiracy, then you can fall into a different cognitive trap that is just as bad as uncritical acceptance.
