Yes by sitting to it, it can hurt the back...but if you are literally flowing with the trot, as if you are "trotting" yourself you're seat will be moving with him...there will be no bounce at all and no pain for the horse.
My friend from the stables rides her horse since she got her bareback. Only twice have I seen her ride in a saddle...that was for a trail (though normally she goes bareback for it) and the other was for the show (where she HAD to use a saddle). Her horses back is fine and she's owned her for over 2 years.
If you are bouncing even the slightest bit all the time while trotting...yes it definately will ruin the back, but I fail to see how, if you are moving with the horse at the pace they are going, how it would hurt their back.....but maybe I"m not looking at it the right way.
Also I don't always ride bareback. If I'm just doing light work and not really practicing on anything, then I'll go bareback....but if I'm practicing something where I'll need perfect Balance (or if Sonny is purposely trying to throw off my balance) then I use my saddle.