There are several ways to make money, advertisements aren't in game because Sony is doing it out of the kindness of their hearts... having said that I agree a company doesn't want to lose money, but sometimes it pays off to take a momentary lose, if you make up that loss later on (eg. free trial periods).
Anarchy Online does fairly decent with their free strategy from what I've gathered but... to get the full game you have to buy it. There's a lot of zones, items, weapons, skills that you don't get if you just play the free version.
I don't think MXO could do that now.. but I really think if more people played Matrix Online they would like it (after CR2.0). The question is how do you bring them here, after such an abyssmal launch/reputation of MXO and SOE?