I agree, ATF is hydraulic fluid, and so it may be suitable for use in a hydraulically dampened suspension. But... the viscosity of ATF is much thicker than what the FJRs forks were designed for. (Edit- there are a few examples of ATF viscosity in the chart linked to by MCRIDER above).
That means that the amount of damping you get at a particular orifice opening will be more, so you may not be able to adjust the clickers enough to get optimal damping. Also, those clickers only adjust the low speed damping. The high speed damping is set internally with fixed orifices and flexible shim stacks, so your high speed damping will definitely be too high with ATF unless you do some major fork revalving. I just use the ATF to flush the forks out, drain it out well, and then put in some good suspension fluid of close to the same viscosity as the Yamaha stuff.