If I purchase a ticket with a Frequent Flyer fare, or tickets issued under other commercial programs promoted by airlines or tour operators, do I lose the ability to protect my rights in the event of denied boarding?

No. All passengers in possession of tickets purchased with a Frequent Flyer fare, or tickets issued in the framework of other commercial programs promoted by airlines or tour operators with confirmed reservations, can protect their rights in the cases indicated above as provided for by Reg. (EC) n. 261/04. 261/04.