"The two organizations that I know which offer rides in a B-17 are the Collings Foundation, Stow, Massachusetts ("Nine-O-Nine" - Collings also has a flying B-24J) and the National Warplane Museum in Horseheads, NY (" Fuddy Duddy").
These planes are often flown to air shows around the USA for static and flying displays, and rides are sold to raise some of the money needed to maintain these amazing aircraft in flying condition (a very expensive proposition as you might imagine).
There are around fourteen B-17's preserved in flying condition around the world (e.g., Confederate Air Force has one), but as far as I know, these are the only two that offer rides to the general public. Organizations like these are preserving an important part of aviation history, mainly through the efforts of volunteers and through membership support.
Visit the web sites to check on schedules, membership, and ride information.