It seems that the directory for the iOS Simulator has changed. It used to be in ~/Library/Application\\ Support/iPhone\\ Simulator/
and now it\'s in ~/Lib
For those who struggling with untrusted connections on Xcode 9 beta's simulators:
I don't know if install script works or not but you are able to install charles' cert in same way as on physical device - through Safari.
Last step that is needed (of course after installing certificate either through script or via Safari): Go to Simluator's settings -> general -> about -> Certificate trust settings -> Charles Proxy Custom Root... -> enable