It will only be present in apps where the developer chooses an ad-based model. I sincerely doubt Apple is going to stick ads in their basic apps (like Mail or Contacts). And I'm guessing most developers will go the way they have up until now -- you can choose a paid version of the app with no ads or a free version with ads. I also don't believe Apple will require developers to use iAds -- if they have their own mechanism for delivering ads, I'm sure they can keep using it.
ETA: Apple is going to be taking 40% and giving the developer 60%, not the other way around. I'm not familiar with the economics of on-line ads, so I don't know how that compares to the rates for other ad brokers.