Apple isn't so much concerned with people porting iPhone apps to other platforms as they are apps targeting a lowest common denominator feature set, or targeting a meta-platform feature set instead of the iPhone SDK feature set.
I just semi-ranted about this on reddit, but my best example at the moment relates to the "XBOX Live" features coming for games in iPhone OS 4. What motivation would Adobe have to Adopt these features in CS5? How long would it take Adobe to adopt these features (if at all)? What if Adobe instead wanted to create their own "XBOX Live" system? Apple would be at the whim of the business interest of the meta-platform, much like they are with Flash on OSX.
After all, Flash devs are going to stay Flash devs, they're not going to port everything to Obj-C just to get one or two features on one platform they're deploying on, they're going to stick with what their meta-platform provides. Apple knows this and they don't want to be stuck the hoping meta-platform want's to move at the same pace they do.
Thats what Apple is talking about when they say these cross-platform apps suck, and if you look at the big ones out there for the desktop (eg, Eclipse, Firefox), they're right, those apps don't take advantage of the OSX features (CoreData, CoreAnimation, GrandCentral), they take advantage of the meta-platform features.