I do work with autistic kids.
"Would it be more beneficial for him not to be flying out to see his Dad?"
Not unattended by an adult capable of handling his issues.
"I do understand that routine is very important for him and is this transition form house to house far to much?"
How old is he and what kind of meds/treatment is he getting?
"Or is it doing more harm having him not come?"
No visitation with Dad will definitely cause more harm than good.
"Would Dad flying to him be a better option?"
That is an excellent idea until he is in a good treatment program for kids with autism and a qualified therapist that works with kids with his issues says he is ready to fly on his own.
"Since the last incident on the plane, (Which his mother booked him as unaccompanied), she does not want to send him. Is that a good idea?"
Until a good plan can be in place for his issues, yes. Either Dad flies there and accompanies him back or mom flies with him to Dad's, or Dad just visits there. This child may never be able to fly on his own. There are too many issues that come up that an autistic person may not be able to handle. Given his issues I am surprised the airline allowed Mom to book his ticket that way.
Also, I should mention he isn't abusing his siblings to be abusive. Autistic kids have little if any impulse control and major sensory issues. They are reactionary to their environments and personal boundaries can be non-existent. It is likely he lacks the insight that his behavior is harmful depending on his age. That is why behavior modification is SO important with these kids.
"That's just my opinion, then again I might be wrong." Dennis Miller