There is no rail line to Courmayeur, the closest point would be Aosta, then a bus from there. It is a very long way around, mostly through Italy. Zermatt to Brig to Domodossola to Milan to Chivasso to Ivrea to Aosta, with only the Zermatt to Domodossola portion covered by the Swiss Travel Pass. Then there is the iffy cable car from Courmayeur to Mont Blanc (iffy because of seasonality, weather shut-downs, maintenance) then cable car to Chamonix, then train to Geneva. Or by bus Courmayeur to Chamonix, none covered by Swiss Travel Pass.
On the other hand, you can go from Zermatt to Chamonix more direct by rail and covered by Swiss Travel Pass. Visit Mont Blanc up and down via year round cable car. Shuttle van direct to Geneva, non of which is covered.