FPV Freerider uses Unity Playerprefs to store the custom settings.
On Linux, PlayerPrefs can be found in ~/.config/unity3d/[CompanyName]/[ProductName]
It should be something like ~/.config/unity3d/Freeride/FPVFreeriderRecharged
Perhaps there is some permissions issue. I'm not a linux user myself though, so I'm not going to be of much help with linux stuff. Please note that the linux version is experimental and may not work on all distributions.