It has to do with the weight shift during braking. Stomp on the rear brake alone and the forks dive as weight shifts to the front of the bike. This is the basis of so many rear wheel lock-ups on the older Rockets with non-integrated brakes. As the rear tire unloads the friction forces are overcome and the tire slides happily down the road. The more weight that shifts the faster the rear tire loses traction. If you've seen someone pull a stoppie the rear tire has 0% stopping power when it's dangling 2 feet in the air. On lighter bikes the weight shift is lower because less mass to start but the stopping force ratio is about the same. If you ride with a passenger you get the benefit of some of their weight over the rear tire but the forks will still dive on hard braking due to weight shift. The reason there are two disks in front is that's where most of the stopping power is. On my Speed Triple I can set the riding mode to unlink the brakes so I can use the rear brake alone. This is in TRACK mode. The purpose of this is to trim speed using trail braking technique and is employed by racers. It still shifts the weight of the bike and makes the steering heavier, however is used to trim speed while in the corner. If you watch any MotoGP racing you'll see prior to turn entry most of the riders are on the front brakes hard enough to skip the rear tire off the tarmac. Do that in a corner and you lowside.
If you use mostly rear brakes for stopping that's fine, but in an emergency situation using only the rear brake is where you find the bike gets loose and then applying fronts drops you on the pavement as most riders get completely out of shape. I had the experience of going sideways on my Rocket in 2009 while towing a trailer and stepped on the rear brake coming to a fast stop when the bike in front of me hit his brakes. I let go of the rear brake, straightened out and then hit it again as his bike was coming up fast and same result, went sideways as the trailer tried to pass me. I let go the rear straightened out and grabbed a handfull of front and it stopped with enough control to manuver around the bike in front of me. The people behind me had a pool going on how bad the wreck was going to be, me I had a pool growing in my undershorts during the event. After that I never touched the rear brake again with a trailer on and stopping was easy and controlled. After that experience I have shifted my braking technique to mostly front and use the rear to assist in speed reduction.