My personal opinion is that FastPass is a non-issue. If the people who take FPs didn't have access to them, the vast majority would just be in the Stand-By line. The same number of riders load regardless of which line they come from, the only difference is the FP users have actually chosen to wait longer to board, just they're waiting elsewhere.
There is a psychological impact that people have as a result of the perceived "special status" of people with FPs "bypassing" the Stand-By line, but in reality it is just that... perception. Because the same numbers of people load at the same rate regardless of which line they're in, the end result is both lines are, by nature, shorter.
For Disney, there are gains and losses involved. They gain by having a number of people wandering the parks that would otherwise be stuck in a line so they may be spending more money. They lose by the expenses involved, the FP machines, paper for passes, staff to monitor both the machines and access/egress to the FP lines and probably some additional computer infrastructure to coordinate gate entry with FP use and timings for issuance and availability of FPs. At the end of the day I suspect, knowing Disney, that it works out to a net gain.