Does the front seam of the door line up even with or slightly out from the fender? If it's sticking out in the airstream, that could cause the problem. My truck's door howls when a headwind or right to left crosswind..
Also, my driver's door extends about 3 mm higher than the passenger door, which also seems to help it catch air in a crosswind. I've owned the truck since it was new, and the only accident I've had is where I backed into someone while leaving my driveway.

 

It is right about dead even.

 

If you have the stick on plastic window vents they can cause an annoying hiss a highway speeds...but most likely after 1000's of repeated closings the top of the door or "shark fin" has bent away from sealing well...
Adjust the "shark fin" by rolling down the window and while standing inside the open door w/your knee bracing it pull inward on the top of the door to tighten up the top to the seal...worked for me.

 

What about the other rubber seal that goes all the way around the door it's behind all the plastic trim? Not too sure I follow on the tightening part. I do not have the plastic stick vent things

 

Ttttt

 

What about doing the hinge pins and bushings? Only a couple of bucks from dorman. I have the same problem and was planning on doing them when it warms up a bit. I had a similar problem on my '96 and doing the pins and bushings did the trick.

 

Have not thought about that is there a way to tell of they are worn out?

 

Well u've done everything else but if u open your door and if there is any up and down movement I would say it's the pins and bushings. Also when you close the door you would see the door move up slightly in order to catch the latch. I'm doing my 05 as soon as it warms up and the symptoms are identical to yours. It's a bit of a pain to do just because of the door spring. Getting it back in after doing the pins and bushings is a b***h. I'm sure there's an easy way to do it I just haven't figured it out yet.

 

Im having the same problem on my 06. Ive never noticed an upward or downward movement on the door. where can i get new pins and bushings?

 

Its not the seals, its the cheap thin flimsy sheet metal the door is constructed out of that all new trucks use these days. It doesn't take much before they will bend and lose their air tight seal.

Close the door on a dollar bill towards the top of the door and see if you can slide it in and out between the door and the seal. If you can:

Adjust the catch plate for the door inwards and bend in the top of the door as described previously in this thread. Some may squirm at that suggestion but the bending been done for years in the autobody industry.