EU is trying to become a single economic and political entity. Unified currency is certainly one of the many steps that they are taking. Furthermore, negotiating Air Services Agreements as a single entity will be a reality very soon. The reason why the British and US governments are rushing to strike an open skies deal soon is because next year, EU nations will no longer be allowed to negotiate on their own. It will be a reality.
The US domestic market is by far the single largest commercial aviation market. EU "domestic" market would still be smaller than the US doemstic, but it would be sizable and much larger than Canadian and Mexican markets. Thus, even if US can get NAFTA to negotiate as a single entity, it doesn't change the equation by much. Furthermore, NAFTA is strictly an economical entity while EU is more than just an economical entity. It is a political entity, too.