Yes! In the Russian sentence "У тебя было хорошее утро" the subject is "утро", and it is neuter. So, the verb agrees with the subject: "Утро было".
In the English sentence "You had a good morning" the subject is "you".
But note: there is no "had" in the Russian version! There is "was" instead. Think of it this way: "A good morning was at you".