Silicone has too many draw backs. It doesn't breath, so it would get incredibly hot underneath. This cowl is also very thin. Silicone would tear, and or lose it's shape. You have to remember the neck has to stretch all the way over the head, which is terrible for durability in silicone that thin. We're dealing with an "A-list" actor... it has to come of quickly between takes. (The cowl isn't glued down to Ben, but if they decided to glue it to a stunt actor, silicone is also harder to glue.)
It was briefly considered due to the failures in the "turn" of previous incarnations of the bat cowl, but now that they have a method that has been proven to work? Silicone doesn't stand a chance.