You protect fragile equipment by remembering that it is fragile. In the same way that donning a bicycle helmet doesn't make it safe to ride the wrong way down the center of the lane of a major highway, or that putting on the full suit of armour doesn't make an American football player immune to injury, owning and using a padded camera bag (or case) doesn't make your equipment bullet-proof.

Honestly, most of my gear spent most of its time in a plain (unpadded, but compartmented) canvas bag when I was a working pro; the bulk of a padded bag would have been impractical most of the time, given the amount of gear I was carrying. Knowing that the bag is unpadded changes the way you handle it. When I knew that there were likely to be knocks and bumps, I used padded hard-shell cases. (My studio and location lighting never went anywhere except in hard-shell cases, mostly because flash tubes are awfully expensive and nobody back in the day had thought to make a decent protective cover for their heads.)

That doesn't mean you need to treat everything like it is going to shatter at any moment; it just means that you can't treat your cameras and lenses like they were solid blocks of tool steel. Even the best-built, most tank-like professional gear is, in the end, a complex electromechanical optical instrument. Treating your gear with just a little bit of care goes a long way.

(By the way, there's probably a lot more to the story than just, "I took the lens out of my bag and it broke," even if the person who wrote it wasn't completely aware of what else had happened on the way to the failure. As I said, the case doesn't make the gear bullet-proof.)