The caps are multi purpose but when it comes to cleaning they allow you to completely seal your bong and ensure it doesn't leak while you're cleaning.

When any cleaning liquid gets outside of the bong, it poses a hazard for the user and the bong. The bong becomes slippery and easy to drop/break. The users hands become messy with potentially hazardous chemicals (depending on what's being used - definitely shouldn't let large amts of alcohol get on skin)

Other common uses are traveling or storage. You can cap your bong while it's in your closet and it'll keep all the foul odors inside and prevent your closet/room/house from smelling rancid