Your counfounding European Union and Shengen area. Countries can be part of the Shengen Area without being in the European union (like Switzerland, Norway). Furthermore, Croatia, Cyprus and Bulgaria are in the process of joining the Shengen area.

The visa issue is between the European Union and the United State, not the Shengen Area and the United States.

It is like if European Union would require a Visa for inhabitants of Texas, Florida and Washington, even if a visa-free deal with the United States was agreed.