With them being armed and trained properly, I don't see how you could say that they WOULDN'T play a factor. How much of a factor? Who can say?
As for not being on every flight, the other issue is that any potential terrorists will have to take that into account, just in case (since they won't know which flight has a marshall, and which doesn't). In order for them to counter the possiblity that a marshal is on the flight, they will have to get more people on board, and get better forms of weapons on board. Both of those things will make detection and exposure prior to the flight that much more likely, and may deter them altogether.
