CNN states that:
The ban, slated to begin on Friday, only applies to foreign nationals, not American citizens, their immediate family members and legal permanent residents.
Returning travelers will be screened prior to entering the US and asked to self-quarantine for 14 days.
This is also confirmed by The Telegraph and Euronews.
It doesn't appear that any distinction is made between direct flights from Europe or layovers in Europe. The proclamation simply doesn't mention it.
All flights between the USA and mainland Europe have been cancelled or interrupted for the next 30 days as of midnight on Friday, March 13th, and given that the majority of people in Europe or transiting in Europe won't be able to fly to the US (since they won't be permanent residents, citizens, etc.) I would recommend consulting your airline prior to flying to Europe since the onward leg may be cancelled.
Regarding cancellations, Forbes has stated:
If your flight is cancelled by the airline, according to the US Department of Transportation you will be eligible for a cash refund, full stop. The European Union has a similar rule, commonly known as Rule 261, that provides for refunds for any flights that arrive into, travel through, or depart Europe.
You can read the full proclamation on the Whitehouse website.