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We had a thread a couple years ago here about this. There are all kinds of ways and it depends on how many holes you want in the bed and how often you want to remove the flag pole.
the basic idea was to u-bolt a pole or bolt in a receiver for a pole.
Do you want to remove the flag often or can the pole be pretty permanent?
Permanent would be as simple as drilling a couple of holes in the pole, then into the stake pocket. Use some toggle bolts and secure the pole to the bed inside of the stake pocket. Less permanent would be to mount a tube in a similar fashion, then drill the pole and tube for a cross pin.
Either way would secure the pole to the bed, then it would up to the pole if it can handle the drag of the flag at highway speed.