People who live in a glass house shouldn't throw stones?

The meaning is: Don't do things to other people, which would be offensive to you if someone else has done it. I.E. if I live in glass house, and someone would throw a stone at me, then the glass would break and I would have to pay a lot of money to fix it, so I shouldn't to the same thing to others and throw stones at people's houses. (Even if the don't live in glass houses, there might be other reasons why it's bad)

The main issue here is, I think, that nothing is certain and if something offensive to you, it may be also offensive to other people for totally different reasons.

Yeah, but why would you live in a glass house? Or throw stones in your house?

The moral isn't literally meaning about throwing stones in glass houses. it's more about doing something then telling someone else not to do it.