High priced reservation fees

If you book with the actual operator of the service instead of a third party (Rail Europe in this case), then you can escape the gratuitous fees.

Easy. Don't use Rail Europe. Use the rail operators. Start at http://www.sbb.ch/en/home.html. The Bernina Express is actually run by the Rhaetian railway, https://www.rhb.ch/en/home, and the Glacier Express is a partnership of the Rhaetian Railway and the Matterhorn-Gotthard-Bahn and has its own website, https://www.glacierexpress.ch/en/

Reservation fees vary according to the season.

and with those high reservation fees on top of the rial pass, the rail pass may not be a bargain. Price the point to point tickets you need, which usually include the reservation, and compare.

Rail Europe's online prices are stated to be available "online only." Every product costs more if you want to book by phone, as well as there is a phone service fee. Sounds like you chose the pass for 15 consecutive days.

The correct price is the one on the SBB (Swiss Railways) site: http://www.sbb.ch/en/leisure-holidays/holidays--short-breaks-in-switzerland/swisstravelsystem/swiss-travel-pass.html

3 days CHF 216
4 days CHF 259
8 days CHF 376
15 days CHF 458

Above prices are second class. You can either buy on the SBB website, or at the airport or border station when you arrive in Switzerland. Same prices apply.
You say you were quoted "550.00", is that Franks or some other currency, you don't say? If you were quoted any more than the SBB price, there is a mark-up.
Reservations are only needed for the tourist trains (Gotthard Express, Bernina Express, Glacier Express and Golden Pass Express). Other than that there are no reservations on any trains in Switzerland. Note that there are other regular trains, every hour on these routes and every other rail line in Switzerland. So you don't have to book, you can just turn up with your pass and catch the normal trains, but you may have to change trains if you do so.
If you want to go on one of these special trains, just book reservations at the operator's website (as listed by Sam).

The "reservation" fees are more like supplements for trains with seating in panorama cars. The seats come with headsets so you can listen to a narration of the sights passing by in a variety of languages.

Just jump on a normal train that travels the same routes/tracks as the Special train and then there's no additional fee required.