You need to do something to it. What to do? There's a million ways to fight it.
The most basic would be to blast the whole underside with WD40 or oil on a regular basis. If it's oiled, it won't rust. WD and oil don't last very long in a wet environment though.
There are more "clingy" type products like Amsoil HDMP, Fluidfilm, etc. There is a thread here with reviews of these types of products. I used Fluidfilm on my old truck and it worked pretty well. It definitely slowed the rust in my doors on my old truck. It was a bit messy, and kind of stinky for a few weeks though. I've sprayed some fluid film into the bottom seam of the Raptor's tailgate, as I noticed some surface rust starting in there already.
Then you get into rust converters, which will stop/kill the rust. I used Mar Hyde One Step on my old truck and have sprayed some leftover onto the Raptor's hitch after I dropped the spare tire to inspect it. You should top coat the area after the rust has been converted for best results.
There are product lines that have both converters and top coats. POR, Rustbullet etc. POR is expensive, Rustbullet is cheap.
There's nothing you can do to totally stop all the rust except for driving through a 2 foot deep puddle of motor oil everyday. The best solution in my mind is to take the bed off and go after it that way. You can get to all the the bed bottom, wheel well areas and cross supports that way, and have good access to the frame and cross members. Pressure wash it, do the rust converter, then top coat it with paint or some type of undercoating/bedliner.
Check the "tape" on the inner part of your rockers too. Replace it if it's starting to peel back and let a bunch of water and salt spray in there. That's a good area to load up with anti-rust treatments, as well as the bottom of all of the doors. Hit the bottom of the radiator core support if you can get to it as well.
