The green is referring to the football pitch that the game is played on. If you have the rub of the green, then you have good luck on the football pitch.
This saying can also be used in golf. When playing golf, the green is the area where the hole is positioned. If you have the rub of the green, then you play a very good hole. In other words, you complete the hole in fewer shots than expected.
I don't think this is a very common phrase. At least, I haven't heard it used that often.