If you're not using a hard-case for transport, it's simply the risk assumed. Given the fact that the hiring standards expected of the people who are piloting our planes have been lowered, it only stands to reason that the hiring standards of those loading cargo and working in other various areas of the aviation industry aren't what it used to be.
I use a club umbrella, disassemble the shaft from the wood heads (if possible) and cross my fingers. Luckily I've avoided issues, but it might have more to do with my practice of including 2-3 towels around the top of the bag to help absorb whatever abuse they might encounter.
Some airlines are definitely better than others. Virgin Atlantic is awesome... wish they would become a domestic US option. Flew with my clubs from London to the US on several occasions, back-and-forth, and was always impressed with how they handled my clubs. Canvas golf club case, at that.