I am wanting to haul my Honda Foreman 500 ES in the box of my Dodge Dakota with the tailgate closed, however, it will not close. Leaving the tailgate down and bouncing through rough terrain may not be good. Any options out there?

if the quad isnt sitting on the tailgate but hits the quad when your trying to close it remove the tailgate and tie the bike in
thats what I would do

I have found that I can fit my Polaris 700 in my dodge ram1500 quadcab shortbox and shut the tailgate, and also prevent it from coming through the rear window. I put an old set of car ramps in and drive up on them, this puts the front wheels against the top rim of the bed holding the quad away from the window.....and the tailgate finally shuts also.