I never said that they are a good thing, I say they are a natural occurrence, something that only can prevented by a very dystopian system.

Because people will always filter what they want to hear and consume, and with that create filter bubbles. If you went to church (regardless of the specific religion) you enter a filter bubble. If you talk with people on a rave you are in a completely different filter bubbles then in a country music bar. Filter bubbles are all around us and yes the Internet is, by its nature, a magnifying glass for this effect. But it inherent to the human nature not inherent to the Internet. So to prevent filter bubbles you would have to radically change the human nature.