I doubt this was intentional but it is rather quite interesting.
First of all, recap, Castiel had just run off to the Middle East to snag some holy oil right? This is important. Then Dean is standing behind talking about how Cas has never gotten it on, Cas looking increasingly uncomfortable.
Cas rubs the back of his neck in nervousness when Dean basically expresses his disbelief at Cas having never been with someone.
Back to the whole visit to the Middle East Cas paid a few minutes ago; in Lebanon and other parts of the Middle East, rubbing the back of your neck towards someone is to express romantic interest in him or her.