Just my experience from talking to people and reading the Cummins forums, about 90% of the transmissions problems come from people that chip the truck and start turning up the power levels. I think this holds true for all the makes, not just Dodge. It seems like a high percentage of the trucks have had some kind of chip on them. My truck came with a chip on it but so far everything is holding up. A transmission has a lot of wear parts in it so you can just expect a rebuild at some point, its just a matter of if its at 80,000 miles or 200,000 miles.
I'd like to say the 5.9 common rail Cummins is bulletproof, but that wouldn't be true. The weak link and one that can cause a engine meltdown is the injectors. Injectors are a wear item and need replaced at some point, usually somewhere between 100,000 and 200,000 miles. People get into problems when they ignore a bad injector and start burning holes in pistons, thinning there oil etc. Hot rodding the truck can also be hard on injectors.