I updated to El Capitan and Freerider no longer works. Does anyone have a solution?

I had an issue with El Capitan where the RX setup went away after setting it up. I deleted the app and reloaded it and that fixed the issue. Have you tried reinstalling?

El Capitan here, and works fine.

doesn't work for me either, tried both versions. is there a way to delete the old prefs perhaps?

There is a way to reset the preferences - press F12 ten times when flying. When you exit back to the menu all preferences will be reset.