Daniel, not silicone, caulk. Like for a house window. I bet Dodge never counted on these trucks lasting long enough to need a redo.
Might want to dig the old stuff out first. If it get rusty around the edges, it will peel out easy.
Mine was the window. If the truck was facing downhill, the water ran over the driprail onto the rubber, then inside around the cab lip, along the trim, to the floor. I thought it was coming in the kick panel vent, I siliconed that, and still had water!