What is the subject in “The zoo and the ice-cream store were the favorite destinations of Sally and Todd?”
The zoo and the ice-cream store is the subject of this sentence. The subject is determined by who or what is doing the action. These two things are actually doing the action by being favorite destinations. The zoo and the ice cream-store were, is the complete noun phrase.
Because the zoo and the ice-cream store are the ones that are being, they are doing the action, this is the subject. Just because Sally and Todd are human beings, does not mean that they are the subject in the sentence. They are the object in this case. This is because the action is happening to them.