Is there away to make airliners not take off or land on certain runways. For example at PHNL no airliner ever takes off from 4R but in the sim they constantly taxi and take off on 4R
I remember there was something called AFCAD or something like that where you were able to select and deselect certain runways. Is that still a thing ? Any ideas ? Thanks 
Not as yet.
There is a new MSFS app called the World Hub, which is nearing release, which should be able to do these types of changes.
There is a new command in the sim in the recent update that may help:
NEW CONTENT/FEATURES
- Added flight plan assistance setting for ATC in the user experience assistance settings so that users can request the ATC to favor their flight plan or world map flight settings over the current conditions. This assistance is set to “Active” by default. Active: ATC will set the active runway and approach for the departure and arrival airport based on the users flight plan or settings in the world map. Deactivated: ATC will set the active runway and approach based on current conditions only.