Hercules are VERY vulnerable to anti-air. While charons are made of glass, hercules are big chunks of glass. As soon as they engage into any warzone, they crumble. I usually escort a hercules with a cloakbot, or I drop units with a hercules beneath a shield, to ensure it lands safely.
Using the same logic, if an enemy uses a hercules to pick up ENEMY units instead, use hacksaws or raiders or any decent anti-air. It's... just one thing you have to watch out for. I think that hercules kidnaps are funny, and they don't seem too hard to deal with.
Good luck, commander!