What I was thinking about doing was taking the flaps out and leaving the vent there. The flaps are really thin rubber and I could probably just pull them out with needle nose pliers. The only problem I could see with that is driving on gravel or dirt roads. I imagine that a lot of dust is swirling around between the cab and the bed and would no doubt get sucked into the cab under the right conditions. The other problem is they pop in from the outside and once I remove them, there is no getting them back in without taking the bed off.
Thanks for all the responses (the ones that weren't dissing my truck...j/p)
David