The "trans flunsh machines will hurt your transmission" myth was created and continues to be propagated by independent transmission repair facilities. Flush machines aren't cheap and most trans shops don't really want to shell out the dough to purchase one. Cost is especially important considering maintaince items like trans flushes don't bring in much cash: Maybe an hours labor and a small mark-up on the fluid. Why do you visit a trans shop? Because you're trans is already borked! Not much up-sell potential there. Compare this to the typical dealership, who's customer traffic makes possible the all important up-sell.
Plain and simple, trans shops make their paycheck replacing and rebuilding transmissions, not replacing fluid with an expensive machine.
Why do they bad-mouth flush machines? Who knows. Maybe it's because they simply don't have one? Here's an idea... all that trans shops see are broken transmissions. When a trans starts slipping, what is the first instinct of many people? Change the fluid! Does this fix the problem? Usually... no. Was it the trans fluid change that caused the trans to finally give it up? Probably not, given that fact it was already slipping.
I know this doesn't sound foreign to many of you. I've heard it from my own dad since I was a teenager, "You don't change the trans fluid in an old trans. The detergents will clean the friction material and cause it to start slipping." The flush machine is just the latest method for doing fluid changes and gets the blame these days.