I've heard this argument before and I've never understood it. Would it make sense to suggest that we ignore the recommendations on Netflix because we'd be missing out on movies we know we wouldn't enjoy? Information overload is becoming a huge problem, and personalization is the solution to the problem, although the problem is a hard one to solve.
Personalization in entertainment is one thing; but it becomes a problem when personalization extends to news, i.e. the information about the world that we use to make civic decisions.
Having news that doesn't interest me show up in my news aggregator of choice doesn't magically make me want to read it. If I have a bias, I'm going to apply it to a set of news articles either way, so I might as well use something that does that work for me.
The filter bubble is just a dumb meme that's running around right now because of book sales and the like.
The real point is that business models based around personalization don't make any sense. I wouldn't worry about it, because none of these systems are going to succeed.
The 20th century and the era of big media was a fluke to begin with. It was a rare and transient state, and it is no more.
