Not sure how beeswax wrappers can be unhygenic. The only thing I ever use them for are sandwiches, made-up begals, etc. So, when I get back home just give them a good soak in cold water, and they are perfectly clean and ready for re-use. I love them, find them so easy (and ethical) to use. Never thought about making my own. Might give that a go sometime.
Never covered a yoghurt pot. So cannot make any comment about that - however, using non-plastic re-usable covers in 'fridge for pasta, salad, rice, second servings of meals, etc. etc. has always been very sucessful.