I've heard from lots of people not to do flushes unless they have been done continuously since it was new just drain and refill the retards at jiffy lube places and wal-mart service have no brains... dont believe their lies!
This is a sort of blanket statement that has evolved from various sources; basically its both valid and not valid.
Most of the time the Domestic and older non-Domestic transmissions do not respond well to fluid flushes, particularly if they have not been done regularly as the owner's manual/FSM states. The older units tend to have more clearance, deposit build-up, and gunk that seals the whole thing together. Very similar to that ideaology that synthetics cause vehicles to leak (this was true on older vehicles, not so much newer ones.)
That being said, the other part to this is the TYPE of flushing being done. Most transmission fluid flushing machines are of the exchanger type. This means they use transmission fluid pump pressure to exchange fluid after being hooked inline with the fluid circuit (usually via the cooler lines) and these pose the least risk and damage to your vehicle.
Another type is the back-flushing machine which is hooked up in a reverse flow manner and uses an external pump to force fluid through the system to shake loose deposits and clean the system. This system poses a greater risk on many levels, the first being that the back flushing can shake loose large deposits and debris in older non-regularly serviced transmissions which can block ports, filters, and cause issues. The second issue they pose is that if done improperly you could over-pressurize the system and possibly affect the seals (many of the seals are meant to be one way), this is an unlikely effect, but not impossible on older non-regularly serviced units.
The final type is actually the same back-flush style system but it uses a heavy duty solvent to clean out the system rather than fresh fluid and causes the same issues as the above system at a higher risk for non-regularly serviced units because the strength of the chemical can sometimes degrade aged seals, worn clutch material, and loosen large chunks of baked/caked on deposits.
In short, if the transmission has not been serviced regularly I would recommend a drain and fill a few times until the fluid is fresh. IF you decide to use a transmision fluid additive while drain and filling to clean out the transmission, make sure you flush the fluid as best as possible as many of those additives are not meant for prolonged use (i.e. SeaFoam) Also, using a Transmission flush machine of the Fluid Exchanger type won't hurt the vehicle anymore than a Drain and Fill. But I would recommend you stay away from the latter two types of machines for older units and even newer units. Toyota actually does not want the latter two types being used on their transmissions due to their own testing and results according to the factory service reps.