The reasoning you will hear is that if the transmission has been neglected/abused and there are deposits in the lines/pathways, by doing a flush it is possible those deposits will become dislodged and clog very small passageways, leading to trans issues.
However, this isn't necessarily true. First, not all flushing machines are created equal.
There are flushing machines that force fluid under pressure into the trans.
There are flushing machines that will simply let the transmission's own pump do the fluid transfer. These are the kinds you want to utilize. They will suck in fresh fluid from one end and dump the old one the other end. As far as I know the fluid is still pressurized as to not overwork the pump, but it is not forced/rushed in.
If the fluid color looks fine, and doesn't smell burnt, odds are you won't have any issues with a trans flush.
Call the place you choose to perform this and check with them what type of machine they use.