This may be stupid question, but I am looking at Ninject sources and don\'t see NInject registering its own controller factory. I also don\'t see any IControllerFactor
MVC3 now recommends the usage of the IDependencyResolver interface instead of the good old IControllerFactory when dealing with DI. You can look at more details of this interface here.
This is the new Ninject class responsible for injecting the dependencies.